Mercurial > repos > galaxyp > pmd_fdr
annotate PMD_FDR_package_for_Galaxy.R @ 0:5cc0c32d05a2 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
author | galaxyp |
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date | Mon, 07 Oct 2019 11:59:37 -0400 |
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children | 460edeedeb7d |
rev | line source |
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0
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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1 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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2 # PMD_FDR_package_for_Galaxy.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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3 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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4 # Project 021 - PMD-FDR for Galaxy-P # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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5 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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6 # Description: Computes iFDR and gFDR on PSMs as a script designed for Galaxy # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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7 # Note that plotting code has been left in that is not used # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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8 # in this file; this is the code I used to create figures for # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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9 # publication. I left it in for potential development of views. # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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10 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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11 # This file was created by concatenating the following files: # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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12 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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13 # A - 005 - Parser - ArgParser.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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14 # B - 019 - PMD-FDR - functions.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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15 # C - 021 - PMD-FDR Wrapper - functions.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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16 # D - 021 - PMD-FDR Main.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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17 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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18 # Required packages: argparser # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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19 # stringr # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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20 # RUnit # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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21 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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22 # Release date: 2019-10-05 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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23 # Version: 1.4 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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24 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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25 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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26 # Package currently supports the following parameters: |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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27 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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28 # --psm_report full name and path to the PSM report |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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29 # --psm_report_1_percent full name and path to the PSM report for 1% FDR |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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30 # --output_i_fdr full name and path to the i-FDR output file |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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31 # --output_g_fdr full name and path to the g-FDR output file |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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32 # --output_densities full name and path to the densities output file |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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33 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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34 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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35 # A - 005 - Parser - ArgParser.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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36 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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37 # Description: Wrapper for argparser package, using RefClass # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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38 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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39 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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40 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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41 #install.packages("argparser") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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42 library(argparser) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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43 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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44 # Class definition |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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45 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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46 ArgParser <- setRefClass("ArgParser", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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47 fields = c("parser")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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48 ArgParser$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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49 initialize = function(...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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50 parser <<- arg_parser(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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51 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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52 local_add_argument = function(...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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53 parser <<- add_argument(parser, ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
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54 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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55 parse_arguments = function(...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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56 result = parse_args(parser, ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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57 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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58 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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59 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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60 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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61 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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62 # B - 019 - PMD-FDR - functions.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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63 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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64 # Primary work-horse for PMD-FDR # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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65 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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66 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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67 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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68 ####### Load libraries etc. |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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69 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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70 library(stringr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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71 library(RUnit) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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72 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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73 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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74 ####### Global values (should be parameters to module but aren't yet) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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75 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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76 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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77 MIN_GOOD_PEPTIDE_LENGTH <- 11 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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78 MIN_ACCEPTABLE_POINTS_IN_DENSITY <- 10 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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79 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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80 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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81 ####### General purpose functions |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
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82 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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83 # Creates a more useful error report when file is not reasonable |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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84 safe_file_exists <- function(file_path){ # Still not particularly useful in cases where it is a valid directory |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
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85 tryCatch( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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86 return(file_test(op = "-f", x=file_path)), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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87 error=function(e) {simpleError(sprintf("file path is not valid: '%s'", file_path))} |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
88 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
89 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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90 # My standard way of loading data into data.frames |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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91 load_standard_df <- function(file_path=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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92 clean_field_names = function(field_names){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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93 result <- field_names |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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94 idx_blank <- which(result == "") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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95 result[idx_blank] <- sprintf("<Field %d>", idx_blank) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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96 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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97 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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98 if (safe_file_exists(file_path)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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99 field_names <- read_field_names(file_path, sep = "\t") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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100 field_names <- clean_field_names(field_names) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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101 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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102 if (length(field_names) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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103 return(data.frame()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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104 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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105 data <- read.table(file = file_path, header = TRUE, sep = "\t", stringsAsFactors = FALSE, blank.lines.skip = TRUE)#, check.names = FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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106 colnames(data) = field_names |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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107 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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108 stop(sprintf("File path does not exist: '%s'", file_path)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
109 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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110 return(data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
111 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
112 save_standard_df <- function(x=NULL, file_path=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
113 if (file_path != ""){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
114 write.table(x = x, file = file_path, quote = FALSE, sep = "\t", row.names = FALSE, col.names = TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
115 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
116 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
117 rename_column <- function(df=NULL, name_before=NULL, name_after=NULL, suppressWarnings=FALSE){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
118 if (is.null(df)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
119 stop("Dataframe (df) does not exist - unable to rename column") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
120 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
121 if (name_before %in% colnames(df)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
122 df[,name_after] <- df[,name_before] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
123 df[,name_before] <- NULL |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
124 } else if (!suppressWarnings){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
125 warning(sprintf("'%s' is not a field in the data frame and so has not been renamed", name_before)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
126 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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127 return(df) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
128 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
129 rename_columns <- function(df=NULL, names_before=NULL, names_after=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
130 for (i in safe_iterator(length(names_before))){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
131 df <- rename_column(df, names_before[i], names_after[i]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
132 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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133 return(df) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
134 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
135 round_to_tolerance <- function(x=NULL, tolerance=NULL, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
136 return(function_to_tolerance(x=x, tolerance=tolerance, FUN=round, ...)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
137 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
138 function_to_tolerance <- function(x=NULL, tolerance=NULL, FUN=NULL, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
139 return(FUN(x/tolerance, ...) * tolerance) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
140 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
141 safe_median <- function(x) median(x, na.rm=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
142 normalize_density <- function(d){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
143 # Normalizes y-values in density function |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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144 # so that the integral under the curve is 1 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
145 # (uses rectangles to approximate area) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
146 delta_x <- diff(range(d$x)) / length(d$x) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
147 unnormalized_integral <- delta_x * sum(d$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
148 new_d <- d |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
149 new_d$y <- with(new_d, y ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
150 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
151 return(new_d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
152 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
153 if_null <- function(cond=NULL, null_result=NULL, not_null_result=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
154 return(switch(1+is.null(cond), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
155 not_null_result, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
156 null_result)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
157 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
158 rainbow_with_fixed_intensity <- function(n=NULL, goal_intensity_0_1=NULL, alpha=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
159 goal_intensity <- 255*goal_intensity_0_1 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
160 hex_colors <- rainbow(n) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
161 rgb_colors <- col2rgb(hex_colors) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
162 df_colors <- data.frame(t(rgb_colors)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
163 df_colors$intensity <- with(df_colors, 0.2989*red + 0.5870*green + 0.1140*blue) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
164 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
165 df_colors$white_black <- with(df_colors, ifelse(intensity < goal_intensity, 255, 0)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
166 df_colors$mix_level <- with(df_colors, (white_black - goal_intensity) / (white_black - intensity ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
167 df_colors$new_red <- with(df_colors, mix_level*red + (1-mix_level)*white_black) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
168 df_colors$new_green <- with(df_colors, mix_level*green + (1-mix_level)*white_black) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
169 df_colors$new_blue <- with(df_colors, mix_level*blue + (1-mix_level)*white_black) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
170 names_pref_new <- c("new_red", "new_green", "new_blue") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
171 names_no_pref <- c("red", "green", "blue") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
172 df_colors <- df_colors[,names_pref_new] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
173 df_colors <- rename_columns(df_colors, names_before = names_pref_new, names_after = names_no_pref) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
174 rgb_colors <-as.matrix(df_colors/255 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
175 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
176 return(rgb(rgb_colors, alpha=alpha)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
177 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
178 safe_iterator <- function(n_steps = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
179 if (n_steps < 1){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
180 result = numeric(0) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
181 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
182 result = 1:n_steps |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
183 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
184 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
185 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
186 col2hex <- function(cols=NULL, col_alpha=255){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
187 if (all(col_alpha<=1)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
188 col_alpha <- round(col_alpha*255) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
189 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
190 col_matrix <- t(col2rgb(cols)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
191 results <- rgb(col_matrix, alpha=col_alpha, maxColorValue = 255) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
192 return(results) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
193 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
194 credible_interval <- function(x=NULL, N=NULL, precision=0.001, alpha=0.05){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
195 # Approximates "highest posterior density interval" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
196 # Uses exact binomial but with a finite list of potential values (1/precision) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
197 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
198 p <- seq(from=0, to=1, by=precision) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
199 d <- dbinom(x = x, size = N, prob = p) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
200 d <- d / sum(d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
201 df <- data.frame(p=p, d=d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
202 df <- df[order(-df$d),] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
203 df$cumsum <- cumsum(df$d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
204 max_idx <- sum(df$cumsum < (1-alpha)) + 1 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
205 max_idx <- min(max_idx, nrow(df)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
206 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
207 lower <- min(df$p[1:max_idx]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
208 upper <- max(df$p[1:max_idx]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
209 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
210 return(c(lower,upper)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
211 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
212 verified_element_of_list <- function(parent_list=NULL, element_name=NULL, object_name=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
213 if (is.null(parent_list[[element_name]])){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
214 if (is.null(object_name)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
215 object_name = "the list" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
216 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
217 stop(sprintf("Element '%s' does not yet exist in %s", element_name, object_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
218 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
219 return(parent_list[[element_name]]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
220 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
221 read_field_names = function(file_path=NULL, sep = "\t"){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
222 con = file(file_path,"r") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
223 fields = readLines(con, n=1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
224 close(con) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
225 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
226 if (length(fields) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
227 return(c()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
228 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
229 fields = strsplit(x = fields, split = sep)[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
230 return(fields) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
231 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
232 check_field_name = function(input_df = NULL, name_of_input_df=NULL, field_name=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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233 test_succeeded <- field_name %in% colnames(input_df) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
234 current_columns <- paste0(colnames(input_df), collapse=", ") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
235 checkTrue(test_succeeded, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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236 msg = sprintf("Expected fieldname '%s' in %s (but did not find it among %s)", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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237 field_name, name_of_input_df, current_columns)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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238 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
239 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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240 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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241 ####### Classes for Data |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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242 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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243 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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244 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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245 # Class: Data_Object |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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246 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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247 Data_Object <- setRefClass("Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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248 fields =list(m_is_dirty = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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249 parents = "list", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
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250 children = "list", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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251 class_name = "character")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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252 Data_Object$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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253 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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254 m_is_dirty <<- TRUE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
255 class_name <<- "Data_Object <abstract class - class_name needs to be set in subclass>" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
256 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
257 load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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258 #print(sprintf("Calling %s$load_data()", class_name)) # Useful for debugging |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
259 ensure_parents() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
260 verify() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
261 m_load_data() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
262 set_dirty(new_value = FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
263 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
264 ensure = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
265 if (m_is_dirty){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
266 load_data() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
267 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
268 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
269 set_dirty = function(new_value){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
270 if (new_value != m_is_dirty){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
271 m_is_dirty <<- new_value |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
272 set_children_dirty() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
273 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
274 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
275 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
276 stop(sprintf("verify() is an abstract method - define it in %s before calling load_data()", class_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
277 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
278 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
279 stop(sprintf("m_load_data() is an abstract method - define it in %s before calling load_data()", class_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
280 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
281 append_parent = function(parent=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
282 parents <<- append(parents, parent) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
283 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
284 append_child = function(child=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
285 children <<- append(children, child) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
286 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
287 ensure_parents = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
288 for (parent in parents){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
289 # print(sprintf("Calling %s$ensure()", parent$class_name)) # Useful for debugging |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
290 parent$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
291 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
292 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
293 set_children_dirty = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
294 for (child in children){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
295 child$set_dirty(TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
296 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
297 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
298 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
299 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
300 # Class: Data_Object_Info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
301 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
302 Data_Object_Info <- setRefClass("Data_Object_Info", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
303 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
304 fields =list( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
305 data_file_name_1_percent_FDR = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
306 data_file_name = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
307 data_path_name = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
308 experiment_name = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
309 designation = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
310 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
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|
311 input_file_type = "character" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
312 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
313 #score_field_name = "character" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
314 #collection_name="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
315 #dir_results="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
316 #dir_dataset="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
317 #dataset_designation="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
318 #file_name_dataset="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
319 #file_name_dataset_1_percent="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
320 #experiment_name="character" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
321 ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
322 Data_Object_Info$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
323 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
324 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
325 class_name <<- "Data_Object_Info - <Abstract class - class_name needs to be set in subclass>" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
326 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
327 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
328 checkFieldExists = function(field_name=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
329 field_value <- .self[[field_name]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
330 checkTrue(length(field_value) > 0, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
331 sprintf("Field %s$%s has not been set (and should have been)", class_name, field_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
332 checkTrue(length(field_value) == 1, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
333 sprintf("Field %s$%s has been set to multiple values (and should be a single value)", class_name, field_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
334 checkTrue(field_value != "", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
335 sprintf("Field %s$%s has been set to an empty string (and should not have been)", class_name, field_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
336 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
337 checkFieldExists("data_file_name") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
338 checkFieldExists("data_path_name") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
339 checkFieldExists("experiment_name") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
340 checkFieldExists("designation") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
341 checkFieldExists("input_file_type") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
342 #checkFieldExists("score_field_name") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
343 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
344 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
345 # Nothing to do - this is really a data class |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
346 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
347 file_path = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
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|
348 result <- file.path(data_path_name, data_file_name) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
349 if (length(result) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
350 stop("Unable to validate file path - one or both of path name and file name are missing") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
351 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
352 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
353 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
354 file_path_1_percent_FDR = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
355 local_file_name <- get_data_file_name_1_percent_FDR() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
356 if (length(local_file_name) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
357 result <- "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
358 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
359 result <- file.path(data_path_name, local_file_name) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
360 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
361 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
362 # Continue even if file name is missing - not all analyses have a 1 percent FDR file; this is managed downstream |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
363 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
364 # if (length(result) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
365 # stop("Unable to validate file path - one or both of path name and file name (of 1 percent FDR file) are missing") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
366 # } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
367 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
368 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
369 get_data_file_name_1_percent_FDR = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
370 return(data_file_name_1_percent_FDR) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
371 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
372 collection_name = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
373 result <- sprintf("%s_%s", experiment_name, designation) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
374 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
375 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
376 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
377 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
378 # Class: Data_Object_Info_737_two_step |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
379 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
380 Data_Object_Info_737_two_step <- setRefClass("Data_Object_Info_737_two_step", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
381 contains = "Data_Object_Info", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
382 fields =list()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
383 Data_Object_Info_737_two_step$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
384 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
385 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
386 class_name <<- "Data_Object_Info_737_two_step" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
387 #score_field_name <<- "Confidence [%]" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
388 data_file_name_1_percent_FDR <<- "737_NS_Peptide_Shaker_PSM_Report_Multi_Stage_Two_Step.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
389 data_file_name <<- "737_NS_Peptide_Shaker_Extended_PSM_Report_Multi_Stage_Two_Step.tabular.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
390 data_path_name <<- file.path(".", "Data") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
391 experiment_name <<- "Oral_737_NS" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
392 designation <<- "two_step" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
393 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
394 input_file_type <<- "PSM_Report" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
395 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
396 #data_collection_oral_737_NS_combined$file_name_dataset_1_percent = "737_NS_Peptide_Shaker_PSM_Report_CombinedDB.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
397 #data_collection_oral_737_NS_two_step$file_name_dataset_1_percent = "737_NS_Peptide_Shaker_PSM_Report_Multi_Stage_Two_Step.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
398 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
399 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
400 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
401 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
402 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
403 # Class: Data_Object_Info_737_combined |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
404 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
405 Data_Object_Info_737_combined <- setRefClass("Data_Object_Info_737_combined", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
406 contains = "Data_Object_Info", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
407 fields =list()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
408 Data_Object_Info_737_combined$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
409 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
410 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
411 class_name <<- "Data_Object_Info_737_combined" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
412 #score_field_name <<- "Confidence [%]" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
413 data_file_name_1_percent_FDR <<- "737_NS_Peptide_Shaker_PSM_Report_CombinedDB.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
414 data_file_name <<- "737_NS_Peptide_Shaker_Extended_PSM_Report_CombinedDB.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
415 data_path_name <<- file.path(".", "Data") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
416 experiment_name <<- "Oral_737_NS" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
417 designation <<- "two_step" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
418 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
419 input_file_type <<- "PSM_Report" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
420 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
421 #data_collection_oral_737_NS_combined$file_name_dataset_1_percent = "737_NS_Peptide_Shaker_PSM_Report_CombinedDB.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
422 #data_collection_oral_737_NS_two_step$file_name_dataset_1_percent = "737_NS_Peptide_Shaker_PSM_Report_Multi_Stage_Two_Step.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
423 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
424 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
425 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
426 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
427 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
428 # Class: Data_Object_Pyrococcus_tr |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
429 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
430 Data_Object_Pyrococcus_tr <- setRefClass("Data_Object_Pyrococcus_tr", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
431 contains = "Data_Object_Info", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
432 fields =list()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
433 Data_Object_Pyrococcus_tr$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
434 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
435 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
436 class_name <<- "Data_Object_Pyrococcus_tr" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
437 #score_field_name <<- "Confidence [%]" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
438 data_file_name_1_percent_FDR <<- "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
439 data_file_name <<- "Pfu_traditional_Extended_PSM_Report.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
440 data_path_name <<- file.path(".", "Data") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
441 experiment_name <<- "Pyrococcus" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
442 designation <<- "tr" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
443 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
444 input_file_type <<- "PSM_Report" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
445 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
446 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
447 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
448 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
449 # Class: Data_Object_Mouse_Mutations |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
450 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
451 Data_Object_Mouse_Mutations <- setRefClass("Data_Object_Mouse_Mutations", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
452 contains = "Data_Object_Info", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
453 fields =list()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
454 Data_Object_Mouse_Mutations$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
455 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
456 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
457 class_name <<- "Data_Object_Mouse_Mutations" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
458 #score_field_name <<- "Confidence [%]" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
459 data_file_name_1_percent_FDR <<- "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
460 data_file_name <<- "Combined_DB_Mouse_5PTM.tabular" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
461 data_path_name <<- file.path(".", "Data") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
462 experiment_name <<- "Mouse Mutations" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
463 designation <<- "combined_05" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
464 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
465 input_file_type <<- "PSM_Report" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
466 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
467 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
468 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
469 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
470 # Class: Data_Object_Raw_Data |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
471 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
472 Data_Object_Raw_Data <- setRefClass("Data_Object_Raw_Data", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
473 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
474 fields =list(df = "data.frame")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
475 Data_Object_Raw_Data$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
476 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
477 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
478 class_name <<- "Data_Object_Raw_Data" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
479 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
480 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
481 # Check that file exists before using it |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
482 file_path <- get_info()$file_path() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
483 if (! safe_file_exists(file_path)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
484 stop(sprintf("Raw data file does not exist (%s)", file_path)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
485 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
486 # BUGBUG: Needs to also check the following: |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
487 # - file is tab-delimited |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
488 # - first row is a list of column names |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
489 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
490 set_info = function(info){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
491 parents[["info"]] <<- info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
492 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
493 get_info = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
494 return(verified_element_of_list(parents, "info", "Data_Object_Raw_Data$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
495 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
496 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
497 info <- get_info() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
498 df <<- load_standard_df(info$file_path()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
499 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
500 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
501 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
502 # Class: Data_Object_Raw_1_Percent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
503 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
504 Data_Object_Raw_1_Percent <- setRefClass("Data_Object_Raw_1_Percent", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
505 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
506 fields =list(df = "data.frame")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
507 Data_Object_Raw_1_Percent$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
508 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
509 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
510 class_name <<- "Data_Object_Raw_1_Percent" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
511 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
512 set_info = function(info){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
513 parents[["info"]] <<- info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
514 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
515 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
516 # Do nothing - a missing file name is acceptable for this module and is dealt with in load() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
517 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
518 get_info = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
519 return(verified_element_of_list(parents, "info", "Data_Object_Raw_1_Percent$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
520 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
521 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
522 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
523 info <- get_info() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
524 file_path <- info$file_path_1_percent_FDR() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
525 if (exists()){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
526 df <<- load_standard_df(info$file_path_1_percent_FDR()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
527 } # Note that failing to load is a valid state for this file, leading to not is_dirty. BUGBUG: this could lead to problems if a good file appears later |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
528 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
529 exists = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
530 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
531 info <- get_info() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
532 local_file_name <- info$get_data_file_name_1_percent_FDR() # Check file name not file path |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
533 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
534 if (length(local_file_name) == 0 ){ # variable not set |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
535 result = FALSE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
536 } else if (local_file_name == ""){ # variable set to empty string |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
537 result = FALSE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
538 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
539 result = safe_file_exists(info$file_path_1_percent_FDR()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
540 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
541 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
542 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
543 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
544 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
545 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
546 # Class: Data_Converter |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
547 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
548 Data_Converter <- setRefClass("Data_Converter", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
549 fields =list(class_name = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
550 file_type = "character" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
551 ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
552 Data_Converter$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
553 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
554 class_name <<- "Data_Converter <abstract class - class_name needs to be set in subclass>" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
555 file_type <<- "file_type has not been set before being used <needs to be set in initialize() of subclass>" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
556 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
557 check_raw_fields = function(info=NULL, raw_data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
558 stop(sprintf("check_raw_fields() is an abstract method - define it in %s before calling Data_Object_Data_Converter$load_data()", class_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
559 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
560 convert_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
561 stop(sprintf("convert_data() is an abstract method - define it in %s before calling Data_Object_Data_Converter$load_data()", class_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
562 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
563 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
564 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
565 # Class: Data_Converter_PMD_FDR_input_file |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
566 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
567 Data_Converter_PMD_FDR_input_file <- setRefClass("Data_Converter_PMD_FDR_input_file", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
568 contains = "Data_Converter", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
569 fields =list( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
570 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
571 ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
572 Data_Converter_PMD_FDR_input_file$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
573 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
574 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
575 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
576 class_name <<- "Data_Converter_PMD_FDR_input_file" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
577 file_type <<- "PMD_FDR_file_type" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
578 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
579 check_raw_fields = function(info=NULL, raw_data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
580 data_original <- raw_data$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
581 check_field_name(data_original, "raw_data", "PMD_FDR_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
582 check_field_name(data_original, "raw_data", "PMD_FDR_pmd") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
583 check_field_name(data_original, "raw_data", "PMD_FDR_spectrum_file") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
584 check_field_name(data_original, "raw_data", "PMD_FDR_proteins") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
585 check_field_name(data_original, "raw_data", "PMD_FDR_spectrum_title") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
586 check_field_name(data_original, "raw_data", "PMD_FDR_sequence") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
587 check_field_name(data_original, "raw_data", "PMD_FDR_decoy") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
588 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
589 convert_data = function(info=NULL, raw_data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
590 data_new <- raw_data$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
591 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
592 return(data_new) # Pass through - everything should be in order |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
593 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
594 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
595 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
596 # Class: Data_Converter_PSM_Report |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
597 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
598 Data_Converter_PSM_Report <- setRefClass("Data_Converter_PSM_Report", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
599 contains = "Data_Converter", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
600 fields =list( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
601 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
602 ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
603 Data_Converter_PSM_Report$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
604 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
605 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
606 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
607 class_name <<- "Data_Converter_PSM_Report" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
608 file_type <<- "PSM_Report" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
609 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
610 check_raw_fields = function(info=NULL, raw_data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
611 data_original <- raw_data$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
612 check_field_name(data_original, "raw_data", "Confidence [%]") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
613 check_field_name(data_original, "raw_data", "Precursor m/z Error [ppm]") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
614 check_field_name(data_original, "raw_data", "Spectrum File") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
615 check_field_name(data_original, "raw_data", "Protein(s)") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
616 check_field_name(data_original, "raw_data", "Spectrum Title") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
617 check_field_name(data_original, "raw_data", "Decoy") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
618 check_field_name(data_original, "raw_data", "Sequence") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
619 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
620 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
621 convert_data = function(info=NULL, raw_data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
622 data_new <- raw_data$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
623 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
624 data_new$PMD_FDR_input_score <- data_new[, "Confidence [%]" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
625 data_new$PMD_FDR_pmd <- data_new[, "Precursor m/z Error [ppm]"] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
626 data_new$PMD_FDR_spectrum_file <- data_new[, "Spectrum File" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
627 data_new$PMD_FDR_proteins <- data_new[, "Protein(s)" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
628 data_new$PMD_FDR_spectrum_title <- data_new[, "Spectrum Title" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
629 data_new$PMD_FDR_sequence <- data_new[, "Sequence" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
630 data_new$PMD_FDR_decoy <- data_new[, "Decoy" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
631 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
632 return(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
633 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
634 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
635 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
636 # Class: Data_Converter_MaxQuant_Evidence |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
637 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
638 Data_Converter_MaxQuant_Evidence <- setRefClass("Data_Converter_MaxQuant_Evidence", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
639 contains = "Data_Converter", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
640 fields =list( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
641 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
642 ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
643 Data_Converter_MaxQuant_Evidence$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
644 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
645 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
646 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
647 class_name <<- "Data_Converter_MaxQuant_Evidence" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
648 file_type <<- "MaxQuant_Evidence" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
649 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
650 check_raw_fields = function(info=NULL, raw_data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
651 data_original <- raw_data$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
652 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
653 check_field_name(data_original, "raw_data", "PEP") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
654 check_field_name(data_original, "raw_data", "Mass error [ppm]") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
655 check_field_name(data_original, "raw_data", "Proteins") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
656 check_field_name(data_original, "raw_data", "Retention time") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
657 check_field_name(data_original, "raw_data", "Sequence") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
658 check_field_name(data_original, "raw_data", "Reverse") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
659 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
660 convert_data = function(info=NULL, raw_data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
661 data_new <- raw_data$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
662 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
663 data_new$PMD_FDR_input_score <- 100 * (1 - data_new[, "PEP" ]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
664 data_new$PMD_FDR_pmd <- data_new[, "Mass error [ppm]"] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
665 data_new$PMD_FDR_spectrum_file <- "<place_holder - assumes a single spectra file>" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
666 data_new$PMD_FDR_proteins <- data_new[, "Proteins" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
667 data_new$PMD_FDR_spectrum_title <- data_new[, "Retention time" ] # Used for ordering peptides - not important in MaxQuant since PMD has already been normalized effectively |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
668 data_new$PMD_FDR_sequence <- data_new[, "Sequence" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
669 data_new$PMD_FDR_decoy <- ifelse( data_new[, "Reverse" ] == "+", 1, 0) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
670 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
671 return(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
672 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
673 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
674 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
675 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
676 # Class: Data_Object_Data_Converter |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
677 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
678 Data_Object_Data_Converter <- setRefClass("Data_Object_Data_Converter", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
679 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
680 fields =list(df = "data.frame", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
681 data_converter = "Data_Converter")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
682 Data_Object_Data_Converter$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
683 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
684 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
685 class_name <<- "Data_Object_Data_Converter" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
686 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
687 currently_supported_file_types = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
688 return(c("PSM_Report", "PMD_FDR_input_file")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
689 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
690 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
691 info <- get_info() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
692 raw_data <- get_raw_data() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
693 file_type <- get_info()$input_file_type |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
694 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
695 set_file_type(file_type) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
696 data_converter$check_raw_fields(info=info, raw_data=raw_data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
697 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
698 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
699 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
700 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
701 info <- get_info() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
702 raw_data <- get_raw_data() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
703 file_type <- get_info()$input_file_type |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
704 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
705 df <<- data_converter$convert_data(info=info, raw_data=raw_data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
706 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
707 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
708 set_file_type = function(file_type = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
709 if (file_type == "PSM_Report" ){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
710 data_converter <<- Data_Converter_PSM_Report $new() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
711 } else if (file_type == "PMD_FDR_input_file"){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
712 data_converter <<- Data_Converter_PMD_FDR_input_file$new() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
713 } else if (file_type == "MaxQuant_Evidence"){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
714 data_converter <<- Data_Converter_MaxQuant_Evidence $new() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
715 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
716 stop(sprintf("File type '%s' is not currently supported by PMD-FDR module", file_type)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
717 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
718 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
719 set_info = function(info){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
720 parents[["info"]] <<- info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
721 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
722 get_info = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
723 return(verified_element_of_list(parents, "info", "Data_Object_Data_Converter$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
724 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
725 set_raw_data = function(raw_data){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
726 parents[["raw_data"]] <<- raw_data |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
727 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
728 get_raw_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
729 return(verified_element_of_list(parents, "raw_data", "Data_Object_Data_Converter$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
730 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
731 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
732 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
733 # Class: Data_Object_Groupings |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
734 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
735 Data_Object_Groupings <- setRefClass("Data_Object_Groupings", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
736 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
737 fields =list(df = "data.frame")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
738 Data_Object_Groupings$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
739 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
740 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
741 class_name <<- "Data_Object_Groupings" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
742 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
743 simplify_field_name = function(x=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
744 result <- gsub(pattern = "PMD_FDR_", replacement = "", x = x) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
745 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
746 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
747 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
748 data_original <- get_data_converter()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
749 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
750 check_field_name(data_original, "data_converter", "PMD_FDR_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
751 check_field_name(data_original, "data_converter", "PMD_FDR_pmd") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
752 check_field_name(data_original, "data_converter", "PMD_FDR_spectrum_file") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
753 check_field_name(data_original, "data_converter", "PMD_FDR_proteins") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
754 check_field_name(data_original, "data_converter", "PMD_FDR_spectrum_title") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
755 check_field_name(data_original, "data_converter", "PMD_FDR_sequence") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
756 check_field_name(data_original, "data_converter", "PMD_FDR_decoy") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
757 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
758 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
759 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
760 make_data_groups <- function(data_original=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
761 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
762 # Functions supporting make_data_groups() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
763 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
764 standardize_fields <- function(data=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
765 data_new <- data |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
766 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
767 info <- get_info() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
768 info$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
769 #field_name_of_score <- info$get_field_name_of_score() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
770 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
771 # #data_new <- rename_column(data_new, "Variable Modifications" , "ptm_list") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
772 # data_new <- rename_column(data_new, field_name_of_score , "PMD_FDR_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
773 # data_new <- rename_column(data_new, "Precursor m/z Error [ppm]", "PMD_FDR_pmd") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
774 # #data_new <- rename_column(data_new, "Isotope Number" , "isotope_number") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
775 # #data_new <- rename_column(data_new, "m/z" , "m_z") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
776 # #data_new <- rename_column(data_new, "Measured Charge" , "charge") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
777 # data_new <- rename_column(data_new, "Spectrum File" , "PMD_FDR_spectrum_file") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
778 # data_new <- rename_column(data_new, "Protein(s)" , "PMD_FDR_proteins") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
779 # data_new <- rename_column(data_new, "Spectrum Title" , "PMD_FDR_spectrum_title") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
780 # data_new <- manage_decoy_column(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
781 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
782 # Now managed in Data_Converter |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
783 # data_new$PMD_FDR_input_score <- data_new[, field_name_of_score ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
784 # data_new$PMD_FDR_pmd <- data_new[, "Precursor m/z Error [ppm]"] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
785 # data_new$PMD_FDR_spectrum_file <- data_new[, "Spectrum File" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
786 # data_new$PMD_FDR_proteins <- data_new[, "Protein(s)" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
787 # data_new$PMD_FDR_spectrum_title <- data_new[, "Spectrum Title" ] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
788 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
789 data_new$value <- data_new$PMD_FDR_pmd |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
790 data_new$PMD_FDR_peptide_length <- str_length(data_new$PMD_FDR_sequence) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
791 #data_new$charge_value <- with(data_new, as.numeric(substr(charge, start=1, stop=str_length(charge)-1))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
792 #data_new$measured_mass <- with(data_new, m_z*charge_value) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
793 data_new$PMD_FDR_spectrum_index <- NA |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
794 data_new$PMD_FDR_spectrum_index[order(data_new$PMD_FDR_spectrum_title, na.last = TRUE)] <- 1:nrow(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
795 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
796 return(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
797 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
798 add_grouped_variable <- function(data_groups = data_groups, field_name_to_group = NULL, vec.length.out = NULL, vec.tolerance = NULL, value_format = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
799 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
800 # Support functions for add_grouped_variable() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
801 find_interval_vec <- function(x=NULL, length.out = NULL, tolerance = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
802 q <- quantile(x = x, probs = seq(from=0, to=1, length.out = length.out), na.rm=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
803 q <- round_to_tolerance(q, tolerance = tolerance) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
804 return(q) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
805 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
806 get_group_data_frame <- function(vec=NULL, value_format = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
807 n <- length(vec) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
808 a <- vec[-n] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
809 b <- vec[-1] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
810 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
811 lower <- ifelse(a == b , "eq", NA) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
812 lower <- ifelse(is.na(lower ), "ge", lower) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
813 upper <- ifelse(a == b , "eq", NA) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
814 upper[n-1] <- ifelse(is.na(upper[n-1]), "le", "eq") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
815 upper <- ifelse(is.na(upper ), "lt", upper) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
816 group <- data.frame(list(idx=1:(n-1), a=a, b=b, lower=lower, upper=upper)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
817 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
818 name_format <- sprintf("%%%s_%%%s_%%s_%%s", value_format, value_format) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
819 group$new_var <- with(group, sprintf(name_format, a, b, lower, upper)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
820 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
821 return(group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
822 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
823 merge_group_with_data <- function(data_groups = NULL, group = NULL, vec = NULL, field_name_to_group = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
824 field_name_new <- sprintf("group_%s", simplify_field_name(field_name_to_group)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
825 group_idx <- findInterval(x = data_groups[,field_name_to_group], |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
826 vec = vec, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
827 all.inside=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
828 data_groups$new_var <- group$new_var[group_idx] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
829 data_groups <- rename_column(data_groups, "new_var", field_name_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
830 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
831 # Body of add_grouped_variable() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
832 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
833 vec <- find_interval_vec(x = data_groups[[field_name_to_group]], |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
834 length.out = vec.length.out, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
835 tolerance = vec.tolerance ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
836 group <- get_group_data_frame(vec = vec, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
837 value_format = value_format) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
838 df_new <- merge_group_with_data(data_groups = data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
839 group = group, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
840 vec = vec, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
841 field_name_to_group = field_name_to_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
842 df_new <- add_group_decoy(df_new, field_name_to_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
843 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
844 return(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
845 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
846 add_already_grouped_variable <- function(field_name_to_group = NULL, data_groups = NULL ){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
847 old_name <- field_name_to_group |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
848 new_name <- sprintf("group_%s", simplify_field_name(old_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
849 df_new <- data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
850 df_new[[new_name]] <- data_groups[[old_name]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
851 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
852 df_new <- add_group_decoy(data_groups = df_new, field_name_to_group = field_name_to_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
853 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
854 return(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
855 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
856 add_value_norm <- function(data_groups = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
857 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
858 df_new <- data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
859 df_new$value_norm <- with(df_new, value - median_of_group_index) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
860 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
861 return(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
862 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
863 add_protein_group <-function(data_groups = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
864 data_new <- data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
865 df_group_def <- data.frame(stringsAsFactors = FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
866 list(pattern = c("" , "pfu_" , "cRAP"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
867 group_name = c("human", "pyrococcus", "contaminant"))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
868 for (i in 1:nrow(df_group_def)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
869 idx <- grepl(pattern = df_group_def$pattern[i], |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
870 x = data_new$PMD_FDR_proteins) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
871 data_new$group_proteins[idx] <- df_group_def$group_name[i] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
872 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
873 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
874 data_new <- add_group_decoy(data_groups = data_new, field_name_to_group = "PMD_FDR_proteins") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
875 return(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
876 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
877 add_group_decoy <- function(data_groups=NULL, field_name_to_group=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
878 simple_field_name <- simplify_field_name(field_name_to_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
879 field_name_decoy <- sprintf("group_decoy_%s", simple_field_name) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
880 field_name_group <- sprintf("group_%s", simple_field_name) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
881 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
882 data_groups[[field_name_decoy]] <- with(data_groups, ifelse(PMD_FDR_decoy, "decoy", data_groups[[field_name_group]])) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
883 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
884 return(data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
885 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
886 add_group_training_class <- function(data_groups = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
887 df_new <- data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
888 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
889 lowest_confidence_group <- min(data_groups$group_input_score) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
890 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
891 is_long_enough <- with(df_new, (PMD_FDR_peptide_length >= MIN_GOOD_PEPTIDE_LENGTH) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
892 is_good <- with(df_new, (PMD_FDR_decoy == 0) & (PMD_FDR_input_score == 100) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
893 is_bad <- with(df_new, (PMD_FDR_decoy == 1) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
894 #is_used_to_train <- with(df_new, used_to_find_middle) # BUGBUG: circular definition |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
895 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
896 idx_good <- which(is_good ) # & is_long_enough) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
897 n_good <- length(idx_good) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
898 idx_testing <- idx_good[c(TRUE,FALSE)] # Selects every other item |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
899 idx_training <- setdiff(idx_good, idx_testing) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
900 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
901 #is_good_short <- with(df_new, is_good & !is_long_enough ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
902 #is_good_long <- with(df_new, is_good & is_long_enough ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
903 is_bad_short <- with(df_new, is_bad & !is_long_enough ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
904 is_bad_long <- with(df_new, is_bad & is_long_enough ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
905 #is_good_training <- with(df_new, is_good_long & (used_to_find_middle == TRUE ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
906 #is_good_testing <- with(df_new, is_good_long & (used_to_find_middle == FALSE) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
907 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
908 df_new$group_training_class <- "other_short" # Default |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
909 df_new$group_training_class[is_long_enough ] <- "other_long" # Default (if long enough) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
910 df_new$group_training_class[idx_training ] <- "good_training" # Length does not matter (anymore) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
911 df_new$group_training_class[idx_testing ] <- "good_testing" # Ditto |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
912 #df_new$group_training_class[is_good_short ] <- "good_short" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
913 df_new$group_training_class[is_bad_long ] <- "bad_long" # ...except for "bad" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
914 df_new$group_training_class[is_bad_short ] <- "bad_short" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
915 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
916 df_new <- add_used_to_find_middle( data_groups = df_new ) # Guarantees consistency between duplicated definitions |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
917 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
918 return(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
919 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
920 add_used_to_find_middle <- function(data_groups = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
921 df_new <- data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
922 idx_used <- which(data_groups$group_training_class == "good_training") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
923 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
924 df_new$used_to_find_middle <- FALSE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
925 df_new$used_to_find_middle[idx_used] <- TRUE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
926 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
927 return(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
928 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
929 add_group_spectrum_index <- function(data_groups = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
930 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
931 # Supporting functions for add_group_spectrum_index() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
932 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
933 get_breaks_all <- function(df_new){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
934 # Supporting function(s) for get_breaks_all() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
935 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
936 get_cut_points <- function(data_subset){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
937 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
938 # Supporting function(s) for get_cut_points() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
939 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
940 cut_values <- function(data=NULL, minimum_segment_length=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
941 # using cpt.mean -- Appears to have a memory leak |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
942 #results_cpt <- cpt.mean(data=data, method="PELT", minimum_segment_length=minimum_segment_length) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
943 #results <- results_cpt@cpts |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
944 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
945 # Just look at the end |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
946 #results <- c(length(data)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
947 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
948 # regularly spaced, slightly larger than minimum_segment_length |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
949 n_points <- length(data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
950 n_regions <- floor(n_points / minimum_segment_length) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
951 n_regions <- ifelse(n_regions == 0, 1, n_regions) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
952 results <- round(seq(1, n_points, length.out = n_regions + 1)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
953 results <- results[-1] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
954 return(results) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
955 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
956 remove_last <- function(x){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
957 return(x[-length(x)] ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
958 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
959 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
960 # Main code of for get_cut_points() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
961 max_idx = max(data_subset$PMD_FDR_spectrum_index) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
962 data_sub_sub <- subset(data_subset, group_training_class == "good_training") #(PMD_FDR_input_score==100) & (PMD_FDR_decoy==0)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
963 minimum_segment_length = 50 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
964 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
965 values <- data_sub_sub$value |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
966 n_values <- length(values) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
967 local_to_global_idx <- data_sub_sub$PMD_FDR_spectrum_index |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
968 if (n_values <= minimum_segment_length){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
969 result <- c() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
970 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
971 local_idx <- cut_values(data=values, minimum_segment_length=minimum_segment_length) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
972 result <- local_to_global_idx[local_idx] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
973 result <- remove_last(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
974 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
975 result <- c(result, max_idx) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
976 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
977 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
978 remove_last <- function(vec) { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
979 return(vec[-length(vec)]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
980 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
981 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
982 # Main code of get_breaks_all() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
983 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
984 breaks <- 1 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
985 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
986 files <- unique(df_new$PMD_FDR_spectrum_file) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
987 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
988 for (local_file in files){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
989 data_subset <- subset(df_new, (PMD_FDR_spectrum_file==local_file)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
990 if (nrow(data_subset) > 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
991 breaks <- c(breaks, get_cut_points(data_subset)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
992 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
993 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
994 breaks <- sort(unique(breaks)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
995 breaks <- remove_last(breaks) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
996 breaks <- c(breaks, max(df_new$PMD_FDR_spectrum_index + 1)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
997 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
998 return(breaks) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
999 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1000 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1001 # Main code of add_group_spectrum_index() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1002 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1003 field_name_to_group <- "PMD_FDR_spectrum_index" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1004 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1005 df_new <- data_groups[order(data_groups[[field_name_to_group]]),] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1006 breaks <- get_breaks_all(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1007 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1008 df_new$group_spectrum_index <- cut(x = df_new[[field_name_to_group]], breaks = breaks, right = FALSE, dig.lab = 6) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1009 df_new <- add_group_decoy(data_groups = df_new, field_name_to_group = field_name_to_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1010 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1011 return(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1012 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1013 add_median_of_group_index <-function(data_groups = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1014 field_median <- "median_of_group_index" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1015 data_good <- subset(data_groups, used_to_find_middle ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1016 med <- aggregate(value~group_spectrum_index, data=data_good, FUN=safe_median) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1017 med <- rename_column(med, "value", field_median) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1018 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1019 data_groups[[field_median]] <- NULL |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1020 df_new <- merge(data_groups, med) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1021 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1022 return(df_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1023 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1024 add_1_percent_to_data_groups <- function(data_groups=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1025 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1026 data_new <- data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1027 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1028 if (get_raw_1_percent()$exists()){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1029 # Load 1 percent file |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1030 df_1_percent <- get_raw_1_percent()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1031 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1032 # Get relevant fields |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1033 df_1_percent$is_in_1percent <- TRUE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1034 df_1_percent <- rename_column(df_1_percent, "Spectrum Title", "PMD_FDR_spectrum_title") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1035 df_1_percent <- df_1_percent[,c("PMD_FDR_spectrum_title", "is_in_1percent")] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1036 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1037 # Merge with data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1038 data_new <- merge(data_new, df_1_percent, all.x=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1039 data_new$is_in_1percent[is.na(data_new$is_in_1percent)] <- FALSE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1040 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1041 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1042 # Save results |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1043 return(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1044 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1045 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1046 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1047 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1048 # Main code of make_data_groups() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1049 data_groups <- standardize_fields(data_original) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1050 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1051 data_groups <- add_grouped_variable(field_name_to_group = "PMD_FDR_input_score", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1052 data_groups = data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1053 vec.length.out = 14, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1054 vec.tolerance = 1, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1055 value_format = "03d") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1056 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1057 data_groups <- add_grouped_variable(field_name_to_group = "PMD_FDR_pmd", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1058 data_groups = data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1059 vec.length.out = 21, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1060 vec.tolerance = 0.1, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1061 value_format = "+05.1f") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1062 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1063 data_groups <- add_grouped_variable(field_name_to_group = "PMD_FDR_peptide_length", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1064 data_groups = data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1065 vec.length.out = 11, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1066 vec.tolerance = 1, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1067 value_format = "02d") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1068 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1069 # data_groups <- add_grouped_variable(field_name_to_group = "m_z", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1070 # data_groups = data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1071 # vec.length.out = 11, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1072 # vec.tolerance = 10, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1073 # value_format = "04.0f") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1074 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1075 # data_groups <- add_grouped_variable(field_name_to_group = "measured_mass", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1076 # data_groups = data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1077 # vec.length.out = 11, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1078 # vec.tolerance = 1, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1079 # value_format = "04.0f") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1080 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1081 # data_groups <- add_already_grouped_variable(field_name_to_group = "isotope_number", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1082 # data_groups = data_groups ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1083 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1084 # data_groups <- add_already_grouped_variable(field_name_to_group = "charge", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1085 # data_groups = data_groups ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1086 # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1087 data_groups <- add_already_grouped_variable(field_name_to_group = "PMD_FDR_spectrum_file", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1088 data_groups = data_groups ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1089 data_groups <- add_protein_group(data_groups = data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1090 data_groups <- add_group_training_class( data_groups = data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1091 data_groups <- add_group_spectrum_index( data_groups = data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1092 data_groups <- add_median_of_group_index( data_groups = data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1093 data_groups <- add_value_norm( data_groups = data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1094 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1095 # fields_of_interest <- c("PMD_FDR_input_score", "PMD_FDR_pmd", "m_z", "PMD_FDR_peptide_length", "isotope_number", "charge", "PMD_FDR_spectrum_file", "measured_mass", "PMD_FDR_spectrum_index", "PMD_FDR_proteins") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1096 # fields_of_interest <- c("value", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1097 # "PMD_FDR_decoy", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1098 # "PMD_FDR_spectrum_title", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1099 # "median_of_group_index", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1100 # "value_norm", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1101 # "used_to_find_middle", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1102 # "group_training_class", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1103 # fields_of_interest, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1104 # sprintf("group_%s" , fields_of_interest), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1105 # sprintf("group_decoy_%s", fields_of_interest)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1106 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1107 fields_of_interest <- c("PMD_FDR_input_score", "PMD_FDR_pmd", "PMD_FDR_peptide_length", "PMD_FDR_spectrum_file", "PMD_FDR_spectrum_index", "PMD_FDR_proteins") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1108 fields_of_interest <- c("value", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1109 "PMD_FDR_decoy", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1110 "PMD_FDR_spectrum_title", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1111 "median_of_group_index", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1112 "value_norm", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1113 "used_to_find_middle", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1114 "group_training_class", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1115 fields_of_interest, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1116 sprintf("group_%s" , simplify_field_name(fields_of_interest)), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1117 sprintf("group_decoy_%s", simplify_field_name(fields_of_interest))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1118 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1119 data_groups <- data_groups[,fields_of_interest] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1120 data_groups <- add_1_percent_to_data_groups(data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1121 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1122 return(data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1123 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1124 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1125 data_original <- get_data_converter()$df #parents[[INDEX_OF_ORIGINAL_DATA]]$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1126 df <<- make_data_groups(data_original) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1127 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1128 set_info = function(info){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1129 parents[["info"]] <<- info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1130 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1131 get_info = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1132 return(verified_element_of_list(parents, "info", "Data_Object_Groupings$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1133 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1134 set_data_converter = function(data_converter){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1135 parents[["data_converter"]] <<- data_converter |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1136 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1137 get_data_converter = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1138 return(verified_element_of_list(parents, "data_converter", "Data_Object_Groupings$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1139 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1140 set_raw_1_percent = function(raw_1_percent){ ############## BUGBUG: the 1% file should be using the same file type format as the standard data (but isn't) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1141 parents[["raw_1_percent"]] <<- raw_1_percent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1142 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1143 get_raw_1_percent = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1144 return(verified_element_of_list(parents, "raw_1_percent", "Data_Object_Groupings$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1145 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1146 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1147 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1148 # Class: Data_Object_Individual_FDR |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1149 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1150 Data_Object_Individual_FDR <- setRefClass("Data_Object_Individual_FDR", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1151 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1152 fields =list(df = "data.frame")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1153 Data_Object_Individual_FDR$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1154 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1155 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1156 class_name <<- "Data_Object_Individual_FDR" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1157 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1158 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1159 data_groups = get_data_groups()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1160 densities = get_densities()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1161 alpha = get_alpha()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1162 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1163 check_field_name(data_groups, "data_groups", "value_norm") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1164 check_field_name(data_groups, "data_groups", "group_decoy_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1165 check_field_name(data_groups, "data_groups", "PMD_FDR_peptide_length") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1166 check_field_name(data_groups, "data_groups", "PMD_FDR_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1167 check_field_name(alpha, "alpha", "alpha") # BUGBUG: I'm missing a field here... |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1168 check_field_name(densities, "densities", "x") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1169 check_field_name(densities, "densities", "t") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1170 check_field_name(densities, "densities", "f") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1171 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1172 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1173 set_data_groups = function(parent){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1174 parents[["data_groups"]] <<- parent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1175 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1176 get_data_groups = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1177 return(verified_element_of_list(parents, "data_groups", "Data_Object_Individual_FDR$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1178 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1179 set_densities = function(parent){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1180 parents[["densities"]] <<- parent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1181 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1182 get_densities = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1183 return(verified_element_of_list(parents, "densities", "Data_Object_Individual_FDR$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1184 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1185 set_alpha = function(parent){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1186 parents[["alpha"]] <<- parent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1187 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1188 get_alpha = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1189 return(verified_element_of_list(parents, "alpha", "Data_Object_Individual_FDR$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1190 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1191 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1192 add_FDR_to_data_groups <- function(data_groups=NULL, densities=NULL, alpha=NULL, field_value=NULL, field_decoy_group=NULL, set_decoy_to_1=FALSE){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1193 # Support functions for add_FDR_to_data_groups() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1194 get_group_fdr <- function(group_stats = NULL, data_groups = NULL, densities=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1195 group_fdr <- apply(X = densities, MARGIN = 2, FUN = max) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1196 df_group_fdr <- data.frame(group_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1197 df_group_fdr <- rename_column(df_group_fdr, "group_fdr", "v") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1198 df_group_fdr$group_of_interest <- names(group_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1199 t <- df_group_fdr[df_group_fdr$group_of_interest == "t", "v"] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1200 f <- df_group_fdr[df_group_fdr$group_of_interest == "f", "v"] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1201 df_group_fdr <- subset(df_group_fdr, !(group_of_interest %in% c("x", "t", "f"))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1202 df_group_fdr$group_fdr <-(df_group_fdr$v - t) / (f - t) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1203 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1204 return(df_group_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1205 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1206 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1207 get_mode <- function(x){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1208 d <- density(x) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1209 return(d$x[which.max(d$y)]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1210 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1211 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1212 # Main code for add_FDR_to_data_groups() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1213 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1214 # Set up analysis |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1215 data_new <- data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1216 data_new$value_of_interest <- data_new[,field_value] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1217 data_new$group_of_interest <- data_new[,field_decoy_group] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1218 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1219 data_subset <- subset(data_new, PMD_FDR_peptide_length >= 11) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1220 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1221 # Identify mean PMD_FDR_input_score per group |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1222 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1223 group_input_score <- aggregate(PMD_FDR_input_score~group_of_interest, data=data_subset, FUN=mean) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1224 group_input_score <- rename_column(group_input_score, "PMD_FDR_input_score", "group_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1225 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1226 #group_fdr <- get_group_fdr(data_groups = data_subset, densities=densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1227 group_stats <- merge(alpha, group_input_score) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1228 group_stats <- subset(group_stats, group_of_interest != "PMD_FDR_decoy") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1229 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1230 x=c(0,group_stats$group_input_score) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1231 y=c(1,group_stats$alpha) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1232 FUN_interp <- approxfun(x=x,y=y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1233 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1234 data_new$interpolated_groupwise_FDR <- FUN_interp(data_new$PMD_FDR_input_score) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1235 if (set_decoy_to_1){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1236 data_new$interpolated_groupwise_FDR[data_new$PMD_FDR_decoy == 1] <- 1 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1237 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1238 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1239 return(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1240 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1241 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1242 data_groups = get_data_groups()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1243 densities = get_densities()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1244 alpha = get_alpha()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1245 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1246 d_true <- densities[,c("x", "t")] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1247 d_false <- densities[,c("x", "f")] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1248 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1249 i_fdr <- add_FDR_to_data_groups(data_groups = data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1250 densities = densities, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1251 alpha = alpha, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1252 field_value ="value_norm", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1253 field_decoy_group = "group_decoy_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1254 # Derive local t |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1255 interp_t <- splinefun(x=d_true$x, y=d_true$t) #approxfun(x=d_true$x, y=d_true$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1256 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1257 # Derive local f |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1258 interp_f <- splinefun(x=d_false$x, y=d_false$f) #approxfun(x=d_true$x, y=d_true$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1259 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1260 # Derive local FDR |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1261 i_fdr$t <- interp_t(i_fdr$value_of_interest) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1262 i_fdr$f <- interp_f(i_fdr$value_of_interest) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1263 i_fdr$alpha <- i_fdr$interpolated_groupwise_FDR |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1264 i_fdr$i_fdr <- with(i_fdr, (alpha*f) / (alpha*f + (1-alpha)*t)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1265 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1266 df <<- i_fdr |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1267 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1268 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1269 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1270 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1271 # Class: Data_Object_Densities |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1272 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1273 Data_Object_Densities <- setRefClass("Data_Object_Densities", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1274 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1275 fields =list(df = "data.frame")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1276 Data_Object_Densities$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1277 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1278 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1279 class_name <<- "Data_Object_Densities" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1280 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1281 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1282 df_data_groups <- get_data_groups()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1283 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1284 checkTrue(nrow(df_data_groups) > 0, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1285 msg = "data_groups data frame was empty (and should not have been)") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1286 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1287 check_field_name(df_data_groups, "data_groups", "value_norm") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1288 check_field_name(df_data_groups, "data_groups", "group_decoy_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1289 check_field_name(df_data_groups, "data_groups", "group_training_class") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1290 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1291 set_data_groups = function(parent=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1292 parents[["data_groups"]] <<- parent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1293 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1294 get_data_groups = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1295 return(verified_element_of_list(parent_list = parents, element_name = "data_groups", object_name = "Data_Object_Densities$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1296 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1297 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1298 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1299 # Support functions for make_densities() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1300 set_values_of_interest <- function(df_data_groups=NULL, field_group = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1301 field_value = "value_norm" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1302 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1303 new_data_groups <- get_data_groups()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1304 new_data_groups$value_of_interest <- new_data_groups[,field_value] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1305 new_data_groups$group_of_interest <- new_data_groups[,field_group] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1306 #groups <- sort(unique(new_data_groups$group_of_interest)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1307 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1308 return(new_data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1309 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1310 get_ylim <- function(data_groups=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1311 ylim <- range(data_groups$value_of_interest, na.rm = TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1312 return(ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1313 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1314 make_hit_density <- function(data_subset=NULL, descr_of_df=NULL, ylim=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1315 #stop("Data_Object_Densities$make_hit_density() is untested beyond here") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1316 verify_density = function(data_subset=NULL, value_field=NULL, descr_of_df=NULL, ylim=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1317 values <- data_subset[value_field] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1318 values <- values[! is.na(values)] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1319 if (length(values) < MIN_ACCEPTABLE_POINTS_IN_DENSITY){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1320 stop (sprintf("There are too few valid %s (%d < %d) in %s to be used for calculating a density function", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1321 value_field, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1322 length(values), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1323 MIN_ACCEPTABLE_POINTS_IN_DENSITY, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1324 descr_of_df)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1325 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1326 d <- density(values, from = ylim[1], to = ylim[2]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1327 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1328 return(d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1329 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1330 uniformalize_density <- function(d){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1331 # Reorganizes y-values of density function so that |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1332 # function is monotone increasing to mode |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1333 # and monotone decreasing afterwards |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1334 idx_mode <- which.max(d$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1335 idx_lower <- 1:(idx_mode-1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1336 idx_upper <- idx_mode:length(d$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1337 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1338 values_lower <- d$y[idx_lower] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1339 values_upper <- d$y[idx_upper] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1340 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1341 new_d <- d |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1342 new_d$y <- c(sort(values_lower, decreasing = FALSE), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1343 sort(values_upper, decreasing = TRUE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1344 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1345 return(new_d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1346 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1347 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1348 local_df <- subset(data_subset, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1349 (PMD_FDR_peptide_length >= MIN_GOOD_PEPTIDE_LENGTH) & |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1350 (used_to_find_middle == FALSE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1351 d <- verify_density (data_subset=local_df, value_field = "value_of_interest", descr_of_df = descr_of_df, ylim=ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1352 d <- normalize_density (d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1353 d <- uniformalize_density(d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1354 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1355 return(d) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1356 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1357 make_true_hit_density <- function(data_groups=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1358 d_true <- make_hit_density(data_subset = subset(data_groups, (group_training_class == "good_testing") ), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1359 descr_of_df = "Good-testing dataset", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1360 ylim = get_ylim(data_groups)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1361 return(d_true) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1362 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1363 make_false_hit_density <- function(data_groups=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1364 d_false <- make_hit_density(data_subset = subset(data_groups, (group_training_class == "bad_long") ), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1365 descr_of_df = "Bad-long dataset", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1366 ylim = get_ylim(data_groups)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1367 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1368 return(d_false) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1369 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1370 add_v_densities <- function(data_groups=NULL, densities=NULL, field_group = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1371 groups <- sort(unique(data_groups$group_of_interest)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1372 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1373 new_densities <- densities |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1374 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1375 for (local_group in groups){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1376 d_v <- make_hit_density(data_subset = subset(data_groups, (group_of_interest == local_group)), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1377 descr_of_df = sprintf("subset of data (where %s is '%s')", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1378 field_group, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1379 local_group), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1380 ylim = get_ylim(data_groups)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1381 new_densities[local_group] <- d_v$y |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1382 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1383 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1384 return(new_densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1385 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1386 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1387 # Main section of make_densities() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1388 df_data_groups <- get_data_groups()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1389 new_data_groups <- set_values_of_interest(df_data_groups, field_group = "group_decoy_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1390 d_true <- make_true_hit_density( new_data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1391 d_false <- make_false_hit_density(new_data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1392 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1393 densities <- data.frame(x=d_true$x, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1394 t=d_true$y, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1395 f=d_false$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1396 densities <- add_v_densities(data_groups=new_data_groups, densities=densities, field_group = "group_decoy_input_score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1397 df <<- densities |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1398 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1399 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1400 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1401 # Class: Data_Object_Alpha |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1402 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1403 Data_Object_Alpha <- setRefClass("Data_Object_Alpha", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1404 contains = "Data_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1405 fields =list(df = "data.frame")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1406 Data_Object_Alpha$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1407 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1408 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1409 class_name <<- "Data_Object_Alpha" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1410 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1411 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1412 densities <- get_densities()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1413 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1414 checkTrue(nrow(densities) > 0, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1415 msg = "Densities data.frame was empty (and should not have been)") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1416 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1417 set_densities = function(parent=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1418 parents[["densities"]] <<- parent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1419 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1420 get_densities = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1421 return(verified_element_of_list(parent_list = parents, element_name = "densities", object_name = "Data_Object_Alpha")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1422 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1423 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1424 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1425 densities <- get_densities()$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1426 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1427 max_of_density = apply(X = densities, MARGIN = 2, FUN = max) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1428 df_alpha <- data.frame(stringsAsFactors = FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1429 list(v = max_of_density, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1430 group_of_interest = names(max_of_density))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1431 df_alpha <- subset(df_alpha, group_of_interest != "x") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1432 t <- with(subset(df_alpha, group_of_interest=="t"), v) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1433 f <- with(subset(df_alpha, group_of_interest=="f"), v) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1434 df_alpha$alpha <- with(df_alpha, (t-v)/(t-f)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1435 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1436 alpha <- df_alpha[,c("group_of_interest", "alpha")] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1437 alpha <- subset(alpha, (group_of_interest != "t") & (group_of_interest != "f")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1438 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1439 df <<- alpha |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1440 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1441 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1442 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1443 # Class: Data_Processor |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1444 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1445 Data_Processor <- setRefClass("Data_Processor", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1446 fields =list(info = "Data_Object_Info", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1447 raw_data = "Data_Object_Raw_Data", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1448 raw_1_percent = "Data_Object_Raw_1_Percent", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1449 data_converter = "Data_Object_Data_Converter", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1450 data_groups = "Data_Object_Groupings", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1451 densities = "Data_Object_Densities", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1452 alpha = "Data_Object_Alpha", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1453 i_fdr = "Data_Object_Individual_FDR")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1454 Data_Processor$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1455 initialize = function(p_info=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1456 if (! is.null(p_info)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1457 set_info(p_info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1458 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1459 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1460 set_info = function(p_info=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1461 # This initialization defines all of the dependencies between the various components |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1462 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1463 info <<- p_info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1464 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1465 # raw_data |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1466 raw_data$set_info(info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1467 info$append_child(raw_data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1468 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1469 # raw_1_percent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1470 raw_1_percent$set_info(info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1471 info$append_child(raw_1_percent) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1472 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1473 # data_converter |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1474 data_converter$set_info (info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1475 data_converter$set_raw_data(raw_data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1476 info $append_child (data_converter) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1477 raw_data $append_child (data_converter) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1478 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1479 # data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1480 data_groups$set_info (info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1481 data_groups$set_data_converter(data_converter) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1482 data_groups$set_raw_1_percent (raw_1_percent) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1483 info $append_child (data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1484 data_converter$append_child (data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1485 raw_1_percent $append_child (data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1486 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1487 # densities |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1488 densities $set_data_groups(data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1489 data_groups$append_child (densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1490 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1491 # alpha |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1492 alpha $set_densities(densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1493 densities$append_child (alpha) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1494 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1495 # i_fdr |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1496 i_fdr$set_data_groups(data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1497 i_fdr$set_densities (densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1498 i_fdr$set_alpha (alpha) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1499 data_groups $append_child(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1500 densities $append_child(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1501 alpha $append_child(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1502 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1503 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1504 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1505 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1506 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1507 ####### Classes for Plotting |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1508 ############################################################# |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1509 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1510 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1511 # Class: Plot_Image |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1512 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1513 Plot_Image = setRefClass("Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1514 fields = list(data_processors = "list", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1515 plot_title = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1516 include_text = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1517 include_main = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1518 x.intersp = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1519 y.intersp = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1520 scale = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1521 main = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1522 is_image_container = "logical")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1523 Plot_Image$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1524 initialize = function(p_data_processors = list(), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1525 p_include_main = TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1526 p_include_text = TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1527 p_is_image_container = FALSE){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1528 include_main <<- p_include_main |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1529 include_text <<- p_include_text |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1530 data_processors <<- p_data_processors |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1531 is_image_container <<- p_is_image_container |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1532 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1533 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1534 plot(main="Define plot_image() for subclass") # Abstract function |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1535 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1536 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1537 stop("Need to define function get_n() for subclass") #Abstract function |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1538 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1539 create_standard_main = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1540 needs_main <- function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1541 return(include_text & include_main & !is_image_container) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1542 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1543 if (needs_main()){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1544 collection_name <- data_processors[[1]]$info$collection_name() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1545 main <<- sprintf("%s\n(Dataset: %s; n=%s)", plot_title, collection_name, format(get_n(), big.mark = ",")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1546 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1547 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1548 plot_image_in_window = function(p_scale=NULL, window_height=NULL, window_width=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1549 scale <<- p_scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1550 SIZE_AXIS <- 2.5 * scale # in the units used by mar |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1551 SIZE_MAIN <- 2.5 * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1552 SIZE_NO_MARGIN <- 0.1 * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1553 FONT_SIZE <- 8 * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1554 WINDOW_WIDTH <- window_width * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1555 WINDOW_HEIGHT <- window_height * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1556 X_INTERSP <- 0.5 * scale + 0.4 # manages legend text spacing |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1557 Y_INTERSP <- 0.5 * scale + 0.4 # manages |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1558 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1559 if (include_main){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1560 mar = c(SIZE_AXIS, SIZE_AXIS, SIZE_MAIN , SIZE_NO_MARGIN) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1561 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1562 mar = c(SIZE_AXIS, SIZE_AXIS, SIZE_NO_MARGIN, SIZE_NO_MARGIN) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1563 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1564 mgp = c(SIZE_AXIS/2, SIZE_AXIS/4, 0) # Margin line (mex units) for axis title, axis labels, axis lines |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1565 ps = FONT_SIZE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1566 x.intersp <<- X_INTERSP |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1567 y.intersp <<- Y_INTERSP |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1568 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1569 windows(width = WINDOW_WIDTH, height=WINDOW_HEIGHT) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1570 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1571 old_par <- par(mar=mar, ps=ps, mgp=mgp) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1572 create_standard_main() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1573 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1574 plot_image() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1575 if (!is_image_container){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1576 axis(side=1, labels=include_text, tcl=-0.5, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1577 axis(side=2, labels=include_text, tcl=-0.5, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1578 box(lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1579 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1580 par(old_par) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1581 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1582 plot_image_in_small_window = function(p_scale=1){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1583 plot_image_in_window(p_scale=p_scale, window_height=2, window_width=3.25) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1584 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1585 plot_image_in_large_window = function(p_scale=1, window_height=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1586 plot_image_in_window(p_scale=p_scale, window_height=window_height, window_width=7) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1587 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1588 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1589 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1590 # Class: Legend_Object |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1591 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1592 Legend_Object = setRefClass("Legend_Object", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1593 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1594 fields = list(user_params = "list", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1595 scale = "numeric")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1596 Legend_Object$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1597 initialize = function(p_user_params = NULL, p_scale = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1598 if (is.null(p_user_params)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1599 user_params <<- list() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1600 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1601 user_params <<- p_user_params |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1602 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1603 if (is.null(p_scale)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1604 stop("Legend_Object must have a valid scale") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1605 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1606 scale <<- p_scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1607 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1608 user_params$x <<- if_null(user_params$x , "topleft", user_params$x) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1609 user_params$y <<- if_null(user_params$y , NULL, user_params$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1610 user_params$bty <<- if_null(user_params$bty , "o", user_params$bty) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1611 user_params$lwd <<- if_null(user_params$lwd , NULL, user_params$lwd * scale) # Because we allow NULL, scale must be inside parens |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1612 user_params$seg.len <<- if_null(user_params$seg.len , 3, user_params$seg.len ) * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1613 user_params$box.lwd <<- if_null(user_params$box.lwd , 1, user_params$box.lwd ) * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1614 user_params$x.intersp <<- if_null(user_params$x.intersp, 0.6, user_params$x.intersp) * scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1615 user_params$y.intersp <<- if_null(user_params$y.intersp, 0.4, user_params$y.intersp) * scale + 0.2 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1616 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1617 show = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1618 first_legend = legend(x = user_params$x, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1619 y = user_params$y, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1620 title = "", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1621 legend = user_params$leg, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1622 col = user_params$col, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1623 bty = user_params$bty, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1624 lty = user_params$lty, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1625 lwd = user_params$lwd, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1626 seg.len = user_params$seg.len, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1627 box.lwd = user_params$box.lwd, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1628 x.intersp = user_params$x.intersp, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1629 y.intersp = user_params$y.intersp) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1630 new_x = first_legend$rect$left |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1631 new_y = first_legend$rect$top + first_legend$rect$h * ifelse(scale==1, 0.07, 0.03 - (scale * 0.02)) #switch(scale, 0.01, -0.01, -0.03, -0.05)# (0.07 - 0.09 * ((scale-1)^2))#(0.15 - 0.08*scale)#.07 * (2 - scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1632 legend(x=new_x, y=new_y, title = user_params$title, legend = "", cex=1.15, bty="n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1633 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1634 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1635 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1636 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1637 # Class: Plot_Multiple_Images |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1638 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1639 Plot_Multiple_Images = setRefClass("Plot_Multiple_Images", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1640 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1641 fields = list(n_images_wide = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1642 n_images_tall = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1643 image_list = "list")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1644 Plot_Multiple_Images$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1645 initialize = function(p_n_images_wide=1, p_n_images_tall=2, p_image_list=NULL, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1646 n_images_wide <<- p_n_images_wide |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1647 n_images_tall <<- p_n_images_tall |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1648 image_list <<- p_image_list |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1649 #plot_title <<- "True Hit and False Hit Distributions" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1650 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1651 callSuper(p_is_image_container=TRUE, ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1652 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1653 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1654 # Support functions |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1655 apply_mtext <- function(letter=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1656 line=1.3*scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1657 mtext(letter, side=1, line=line, adj=0) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1658 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1659 # main code |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1660 old_par <- par(mfrow=c(n_images_tall, n_images_wide)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1661 i=0 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1662 n_images <- length(image_list) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1663 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1664 for (i in 1:n_images){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1665 image <- image_list[[i]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1666 image$create_standard_main() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1667 image$scale <- scale |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1668 image$plot_image() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1669 axis(side=1, labels=include_text, tcl=-0.5, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1670 axis(side=2, labels=include_text, tcl=-0.5, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1671 box(lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1672 apply_mtext(letter=sprintf("(%s)", letters[i])) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1673 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1674 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1675 par(old_par) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1676 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1677 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1678 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1679 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1680 # Class: Plot_Compare_PMD_and_Norm_Density |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1681 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1682 Plot_Compare_PMD_and_Norm_Density = setRefClass("Plot_Compare_PMD_and_Norm_Density", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1683 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1684 fields = list(show_norm = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1685 display_n_psms = "logical")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1686 Plot_Compare_PMD_and_Norm_Density$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1687 initialize = function(p_show_norm=TRUE, p_display_n_psms=TRUE, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1688 show_norm <<- p_show_norm |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1689 display_n_psms <<- p_display_n_psms |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1690 plot_title <<- "True Hit and False Hit Distributions" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1691 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1692 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1693 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1694 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1695 # Support functions for plot_compare_PMD_and_norm_density() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1696 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1697 get_densities <- function(data_subset = NULL, var_value = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1698 data_subset$value_of_interest <- data_subset[,var_value] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1699 from <- min(data_subset$value_of_interest, na.rm = TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1700 to <- max(data_subset$value_of_interest, na.rm = TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1701 xlim = range(data_subset$value_of_interest) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1702 data_true <- subset(data_subset, (PMD_FDR_decoy==0) & (PMD_FDR_input_score==100)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1703 data_false <- subset(data_subset, (PMD_FDR_decoy==1)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1704 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1705 d_true <- with(data_true , density(value_of_interest, from = from, to = to, na.rm = TRUE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1706 d_false <- with(data_false, density(value_of_interest, from = from, to = to, na.rm = TRUE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1707 d_true <- normalize_density(d_true) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1708 d_false <- normalize_density(d_false) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1709 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1710 densities <- list(d_true=d_true, d_false=d_false, var_value = var_value, n_true = nrow(data_true), n_false = nrow(data_false)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1711 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1712 return(densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1713 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1714 get_xlim <- function(densities_a = NULL, densities_b = NULL, show_norm=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1715 xlim <- range(c( densities_a$d_true$x, densities_a$d_false$y)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1716 if (show_norm){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1717 xlim <- range(c(xlim, densities_b$d_true$x, densities_b$d_false$y)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1718 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1719 return(xlim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1720 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1721 get_ylim <- function(densities_a = NULL, densities_b = NULL, show_norm=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1722 ylim <- range(c( densities_a$d_true$y, densities_a$d_false$y)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1723 if (show_norm){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1724 ylim <- range(c(ylim, densities_b$d_true$y, densities_b$d_false$y)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1725 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1726 return(ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1727 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1728 plot_distributions <- function(densities = NULL, var_value= NULL, dataset_name = NULL, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1729 leg = list() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1730 leg$leg = c("Good", "Bad") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1731 if (display_n_psms){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1732 leg$leg = sprintf("%s (%d PSMs)", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1733 leg$leg, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1734 c(densities$n_true, densities$n_false)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1735 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1736 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1737 leg$col = c("black", "red") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1738 leg$lwd = c(3 , 3) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1739 leg$lty = c(1 , 2) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1740 leg$title = "Hit Category" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1741 xlab = ifelse(var_value == "value", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1742 "PMD (ppm)", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1743 "PMD - normalized (ppm)") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1744 ylab = "Density" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1745 if (!include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1746 xlab = "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1747 ylab = "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1748 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1749 plot( densities$d_true , col=leg$col[1], lwd=leg$lwd[1] * scale, lty=leg$lty[1], xaxt = "n", yaxt = "n", main=main, xlab = xlab, ylab=ylab, ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1750 lines(densities$d_false, col=leg$col[2], lwd=leg$lwd[2] * scale, lty=leg$lty[2]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1751 abline(v=0, h=0, col="gray", lwd=1*scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1752 if (include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1753 legend_object <- Legend_Object$new(leg, scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1754 legend_object$show() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1755 #legend("topleft", legend=leg.leg, col=leg.col, lwd=leg.lwd, lty=leg.lty, x.intersp = x.intersp, y.intersp = y.intersp) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1756 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1757 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1758 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1759 # Main code block for plot_compare_PMD_and_norm_density |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1760 data_processor <- data_processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1761 data_processor$data_groups$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1762 data_groups <- data_processor$data_groups$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1763 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1764 data_subset_a <- subset(data_groups , used_to_find_middle == FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1765 data_subset_b <- subset(data_subset_a, PMD_FDR_peptide_length > 11) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1766 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1767 densities_a <- get_densities(data_subset = data_subset_a, var_value = "value") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1768 densities_b <- get_densities(data_subset = data_subset_b, var_value = "value_norm") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1769 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1770 xlim=get_xlim(densities_a, densities_b, show_norm = show_norm) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1771 ylim=get_ylim(densities_a, densities_b, show_norm = show_norm) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1772 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1773 dataset_name <- data_processor$info$collection_name |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1774 plot_distributions( densities=densities_a, var_value = "value" , dataset_name = dataset_name, xlim=xlim, ylim=ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1775 if (show_norm){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1776 plot_distributions(densities=densities_b, var_value = "value_norm", dataset_name = dataset_name, xlim=xlim, ylim=ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1777 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1778 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1779 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1780 data_processor <- data_processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1781 data_processor$data_groups$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1782 data_subset_a <- subset(data_processor$data_groups$df , used_to_find_middle == FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1783 data_subset_b <- subset(data_subset_a, PMD_FDR_peptide_length > 11) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1784 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1785 if (show_norm){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1786 data_subset <- data_subset_a |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1787 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1788 data_subset <- data_subset_b |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1789 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1790 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1791 data_true <- subset(data_subset, (PMD_FDR_decoy==0) & (PMD_FDR_input_score==100)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1792 data_false <- subset(data_subset, (PMD_FDR_decoy==1)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1793 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1794 return(nrow(data_true) + nrow(data_false)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1795 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1796 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1797 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1798 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1799 # Class: Plot_Time_Invariance_Alt |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1800 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1801 Plot_Time_Invariance_Alt = setRefClass("Plot_Time_Invariance_Alt", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1802 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1803 fields = list(show_norm = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1804 display_n_psms = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1805 training_class = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1806 ylim = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1807 field_of_interest = "character")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1808 Plot_Time_Invariance_Alt$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1809 initialize = function(p_ylim=NULL, p_training_class=NULL, p_field_of_interest="value_norm", ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1810 get_subset_title <- function(training_class=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1811 if (training_class == "bad_long"){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1812 subset_title="bad only" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1813 } else if (training_class == "good_testing"){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1814 subset_title="good-testing only" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1815 } else if (training_class == "good_training"){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1816 subset_title="good-training only" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1817 } else if (training_class == "other"){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1818 subset_title="other only" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1819 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1820 stop("Unexpected training_class in plot_time_invariance") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1821 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1822 return(subset_title) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1823 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1824 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1825 ylim <<- p_ylim |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1826 training_class <<- p_training_class |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1827 field_of_interest <<- p_field_of_interest |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1828 subset_title <- get_subset_title(training_class=training_class) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1829 backup_title <- sprintf("Middle 25%% PMD for spectra sorted by index%s", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1830 ifelse(is.null(subset_title), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1831 "", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1832 sprintf(" - %s", subset_title))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1833 #plot_title <<- get_main(main_title=main, backup_title=backup_title, data_collection = data_collection) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1834 plot_title <<- backup_title |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1835 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1836 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1837 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1838 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1839 # Support functions for plot_time_invariance() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1840 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1841 # Main code of plot_time_invariance() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1842 data_subset = get_data_subset() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1843 plot_group_spectrum_index_from_subset_boxes(data_subset = data_subset) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1844 abline(h=0, col="blue", lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1845 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1846 get_data_subset = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1847 data_processor <- data_processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1848 data_processor$data_groups$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1849 return(subset(data_processor$data_groups$df, (group_training_class==training_class))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1850 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1851 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1852 return(nrow(get_data_subset())) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1853 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1854 plot_group_spectrum_index_from_subset_boxes = function(data_subset = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1855 n_plot_groups <- 100 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1856 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1857 field_name_text <- ifelse(field_of_interest=="value", "PMD", "Translated PMD") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1858 new_subset <- data_subset |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1859 new_subset$value_of_interest <- new_subset[,field_of_interest] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1860 new_subset <- new_subset[order(new_subset$PMD_FDR_spectrum_index),] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1861 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1862 idxs <- round_to_tolerance(seq(from=1, to=nrow(new_subset), length.out = n_plot_groups+1), 1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1863 idxs_left <- idxs[-(n_plot_groups+1)] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1864 idxs_right <- idxs[-1] - 1 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1865 idxs_right[n_plot_groups] <- idxs_right[n_plot_groups] + 1 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1866 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1867 new_subset$plot_group <- NA |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1868 for (i in 1:n_plot_groups){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1869 new_subset$plot_group[idxs_left[i]:idxs_right[i]] <- i |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1870 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1871 xleft <- aggregate(PMD_FDR_spectrum_index ~plot_group, data=new_subset, FUN=min) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1872 xright <- aggregate(PMD_FDR_spectrum_index ~plot_group, data=new_subset, FUN=max) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1873 ybottom <- aggregate(value_of_interest~plot_group, data=new_subset, FUN=function(x){quantile(x, probs = 0.5 - (0.25/2))}) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1874 ytop <- aggregate(value_of_interest~plot_group, data=new_subset, FUN=function(x){quantile(x, probs = 0.5 + (0.25/2))}) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1875 boxes <- merge( rename_column(xleft , "PMD_FDR_spectrum_index" , "xleft"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1876 merge( rename_column(xright , "PMD_FDR_spectrum_index" , "xright"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1877 merge(rename_column(ybottom, "value_of_interest", "ybottom"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1878 rename_column(ytop , "value_of_interest", "ytop")))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1879 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1880 xlab <- "Spectrum Index" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1881 ylab <- sprintf("%s (ppm)", field_name_text ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1882 if (is.null(ylim)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1883 ylim <<- range(new_subset$value_of_interest) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1884 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1885 if (!include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1886 xlab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1887 ylab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1888 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1889 plot(value_of_interest~PMD_FDR_spectrum_index, data=new_subset, type="n", ylim=ylim, xlab = xlab, ylab=ylab, main=main, xaxt="n", yaxt="n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1890 with(boxes, rect(xleft = xleft, ybottom = ybottom, xright = xright, ytop = ytop, lwd=scale)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1891 #points(median_of_group_index~PMD_FDR_spectrum_index, data=data_subset, cex=.5, pch=15) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1892 axis(1, labels=include_text, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1893 axis(2, labels=include_text, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1894 box(lwd=scale) #box around plot area |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1895 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1896 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1897 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1898 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1899 # Class: Plot_Time_Invariance_Alt_Before_and_After |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1900 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1901 Plot_Time_Invariance_Alt_Before_and_After = setRefClass("Plot_Time_Invariance_Alt_Before_and_After", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1902 contains = "Plot_Multiple_Images", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1903 fields = list()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1904 Plot_Time_Invariance_Alt_Before_and_After$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1905 initialize = function(p_data_processors = NULL, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1906 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1907 p_include_main=FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1908 p_ylim = c(-4,4), ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1909 plot_object1 <- Plot_Time_Invariance_Alt$new(p_data_processors = p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1910 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1911 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1912 p_training_class = "good_testing", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1913 p_field_of_interest = "value", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1914 p_ylim = p_ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1915 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1916 plot_object2 <- Plot_Time_Invariance_Alt$new(p_data_processors = p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1917 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1918 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1919 p_training_class = "good_testing", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1920 p_field_of_interest = "value_norm", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1921 p_ylim = p_ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1922 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1923 callSuper(p_n_images_wide=1, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1924 p_n_images_tall=2, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1925 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1926 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1927 p_image_list = list(plot_object1, plot_object2), ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1928 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1929 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1930 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1931 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1932 # Class: Plot_Density_PMD_and_Norm_Decoy_by_AA_Length |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1933 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1934 Plot_Density_PMD_and_Norm_Decoy_by_AA_Length = setRefClass("Plot_Density_PMD_and_Norm_Decoy_by_AA_Length", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1935 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1936 fields = list(show_norm = "logical")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1937 Plot_Density_PMD_and_Norm_Decoy_by_AA_Length$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1938 initialize = function(p_show_norm=FALSE, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1939 plot_title <<- "The Decoy Bump: PMD Distribution of Decoy matches by peptide length" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1940 show_norm <<- p_show_norm |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1941 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1942 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1943 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1944 data_processor <- data_processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1945 data_processor$data_groups$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1946 data_subset <- subset(data_processor$data_groups$df, (PMD_FDR_decoy == 1)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1947 return(nrow(data_subset)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1948 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1949 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1950 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1951 # Support functions for plot_density_PMD_and_norm_decoy_by_aa_length() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1952 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1953 add_group_peptide_length_special <- function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1954 data_processor <- data_processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1955 data_processor$data_groups$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1956 data_groups <- data_processor$data_groups$df # the name data_groups is a data.frame instead of a Data_Object |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1957 data_groups <- subset(data_groups, used_to_find_middle == FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1958 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1959 df_group_definition <- data.frame(stringsAsFactors = FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1960 list(group_peptide_length_special = c("06-08", "09-10", "11-12", "13-15", "16-20", "21-50"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1961 min = c( 6 , 9 , 11 , 13 , 16 , 21 ), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1962 max = c( 8 , 10 , 12 , 15 , 20 , 50 ) )) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1963 group_peptide_length_special <- data.frame(list(PMD_FDR_peptide_length = 6:50)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1964 group_peptide_length_special$min <- with(group_peptide_length_special, sapply(PMD_FDR_peptide_length, FUN = function(i) max(df_group_definition$min[df_group_definition$min <= i]))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1965 group_peptide_length_special <- merge(group_peptide_length_special, df_group_definition) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1966 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1967 data_groups$group_peptide_length_special <- NULL |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1968 new_data_groups <- (merge(data_groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1969 group_peptide_length_special[,c("PMD_FDR_peptide_length", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1970 "group_peptide_length_special")])) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1971 return(new_data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1972 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1973 get_densities <- function(data_subset = NULL, field_value = NULL, field_group=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1974 get_density_from_subset <- function(data_subset=NULL, xlim=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1975 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1976 d_group <- with(data_subset , density(value_of_interest, from = xlim[1], to = xlim[2], na.rm=TRUE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1977 d_group <- normalize_density(d_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1978 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1979 return(d_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1980 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1981 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1982 data_temp <- data_subset |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1983 data_temp$value_of_interest <- data_temp[[field_value]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1984 data_temp$group_of_interest <- data_temp[[field_group]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1985 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1986 xlim = range(data_temp$value_of_interest, na.rm=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1987 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1988 groups <- sort(unique(data_temp$group_of_interest)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1989 n_groups <- length(groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1990 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1991 d_group <- get_density_from_subset( data_subset=data_temp, xlim = xlim ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1992 densities <- list("All decoys" = d_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1993 for (i in 1:n_groups){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1994 group <- groups[i] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1995 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1996 d_group <- get_density_from_subset( data_subset=subset(data_temp, (group_of_interest == group)), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1997 xlim = xlim ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1998 densities[[group]] <- d_group |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
1999 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2000 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2001 return(densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2002 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2003 get_limits <- function(densities_a = NULL, densities_b = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2004 xlim = c() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2005 ylim = c(0) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2006 for (single_density in densities_a){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2007 xlim=range(c(xlim, single_density$x)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2008 ylim=range(c(ylim, single_density$y)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2009 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2010 for (single_density in densities_b){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2011 xlim=range(c(xlim, single_density$x)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2012 ylim=range(c(ylim, single_density$y)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2013 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2014 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2015 return(list(xlim=xlim, ylim=ylim)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2016 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2017 plot_distributions <- function(data_groups = NULL, xlim=NULL, ylim=NULL, densities = NULL, field_group= NULL, field_value = "value", xlab_modifier = "", var_value= NULL, include_peak_dots=TRUE, dataset_name = NULL, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2018 data_groups$group_of_interest <- data_groups[[field_group]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2019 data_groups$value_of_interest <- data_groups[[field_value]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2020 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2021 # Main body of plot_decoy_distribution_by_field_of_interest() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2022 FIXED_LWD=3 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2023 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2024 groups <- sort(unique(data_groups$group_of_interest)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2025 n <- length(groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2026 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2027 df_leg <- data.frame(stringsAsFactors = FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2028 list(leg = groups, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2029 col = rainbow_with_fixed_intensity(n = n, goal_intensity_0_1 = 0.4), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2030 lty = rep(1:6, length.out=n), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2031 lwd = rep(FIXED_LWD , n)) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2032 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2033 d <- densities[["All decoys"]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2034 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2035 xlab = sprintf("Precursor Mass Discrepancy%s (ppm)", xlab_modifier) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2036 ylab = "Density" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2037 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2038 if (!include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2039 xlab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2040 ylab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2041 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2042 plot(d, lwd=FIXED_LWD * scale, main=main, xlab=xlab, ylab=ylab, xlim=xlim, ylim=ylim, xaxt="n", yaxt="n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2043 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2044 ave_peak <- max(d$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2045 max_peak <- 0 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2046 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2047 for (local_group in groups){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2048 data_subset <- subset(data_groups, group_of_interest == local_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2049 data_info <- subset(df_leg , leg == local_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2050 col <- data_info$col[1] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2051 lty <- data_info$lty[1] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2052 lwd <- data_info$lwd[1] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2053 if (nrow(data_subset) > 100){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2054 d <- densities[[local_group]] #density(data_subset[[field_value]]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2055 lines(d, col=col, lty=lty, lwd=lwd * scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2056 peak <- max(d$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2057 max_peak <- max(max_peak, peak) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2058 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2059 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2060 abline(v=0, h=0, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2061 leg <- list(title = "Peptide length (aa)", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2062 leg = c("All decoys" , df_leg$leg), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2063 col = c(col2hex("black") , df_leg$col), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2064 lty = c(1 , df_leg$lty), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2065 lwd = c(FIXED_LWD , df_leg$lwd) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2066 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2067 if (include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2068 legend_object = Legend_Object$new(leg, scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2069 legend_object$show() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2070 #first_legend = legend(x="topleft", title = "", legend = leg$leg, col = leg$col, lty = leg$lty, lwd = leg$lwd, seg.len=leg$seg.len, box.lwd=leg$box.lwd, x.intersp = leg$x.intersp, y.intersp = leg$y.intersp) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2071 #new_x = first_legend$rect$left |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2072 #new_y = first_legend$rect$top + first_legend$rect$h * .07 * (2 - scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2073 #legend(x=new_x, y=new_y, title = leg$title, legend = "", cex=1.15, bty="n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2074 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2075 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2076 box(lwd=scale) #box around plot area |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2077 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2078 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2079 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2080 # Main body for plot_density_PMD_and_norm_decoy_by_aa_length() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2081 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2082 data_mod <- add_group_peptide_length_special() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2083 data_mod <- subset(data_mod, PMD_FDR_decoy==1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2084 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2085 densities_a <- get_densities(data_subset = data_mod, field_value = "value" , field_group = "group_peptide_length_special") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2086 densities_b <- get_densities(data_subset = data_mod, field_value = "value_norm", field_group = "group_peptide_length_special") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2087 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2088 data_processor <- data_processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2089 dataset_name <- data_processor$info$collection_name() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2090 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2091 limits <- get_limits(densities_a, densities_b) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2092 xlim <- limits$xlim |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2093 ylim <- limits$ylim |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2094 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2095 if (show_norm){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2096 plot_distributions(data_groups = data_mod, densities=densities_b, field_value = "value_norm", xlab_modifier = " - normalized", field_group = "group_peptide_length_special", dataset_name=dataset_name, xlim=xlim, ylim=ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2097 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2098 plot_distributions(data_groups = data_mod, densities=densities_a, field_value = "value" , xlab_modifier = "" , field_group = "group_peptide_length_special", dataset_name=dataset_name, xlim=xlim, ylim=ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2099 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2100 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2101 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2102 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2103 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2104 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2105 # Class: Plot_Bad_CI |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2106 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2107 Plot_Bad_CI = setRefClass("Plot_Bad_CI", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2108 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2109 fields = list(breaks = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2110 ylim = "numeric")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2111 Plot_Bad_CI$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2112 initialize = function(p_breaks=20, p_ylim=NULL, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2113 if (is.null(p_ylim)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2114 ylim <<- numeric(0) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2115 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2116 ylim <<- p_ylim |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2117 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2118 breaks <<- p_breaks |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2119 plot_title <<- "Credible Intervals for proportion within range - bad" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2120 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2121 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2122 data_processor = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2123 return(data_processors[[1]]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2124 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2125 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2126 data_processor()$data_groups$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2127 return(nrow(subset(data_processor()$data_groups$df, (PMD_FDR_decoy == 1)))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2128 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2129 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2130 data_processor()$data_groups$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2131 data_groups <- data_processor()$data_groups$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2132 data_decoy <- subset(data_groups, data_groups$group_training_class == "bad_long") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2133 data_decoy$region <- cut(x = data_decoy$value, breaks = breaks) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2134 table(data_decoy$region) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2135 regions <- unique(data_decoy$region) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2136 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2137 N = nrow(data_decoy) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2138 find_lower_ci_bound <- function(x){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2139 ci <- credible_interval(length(x), N, precision = 0.001, alpha=0.05) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2140 return(ci[1]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2141 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2142 find_upper_ci_bound <- function(x){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2143 ci <- credible_interval(length(x), N, precision = 0.001, alpha=0.05) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2144 return(ci[2]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2145 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2146 xleft <- aggregate(value~region, data=data_decoy, FUN=min) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2147 xright <- aggregate(value~region, data=data_decoy, FUN=max) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2148 ytop <- aggregate(value~region, data=data_decoy, FUN=find_upper_ci_bound) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2149 ybottom <- aggregate(value~region, data=data_decoy, FUN=find_lower_ci_bound) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2150 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2151 xleft <- rename_column(xleft , "value", "xleft" ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2152 xright <- rename_column(xright , "value", "xright" ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2153 ytop <- rename_column(ytop , "value", "ytop" ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2154 ybottom <- rename_column(ybottom, "value", "ybottom") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2155 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2156 boxes <- merge(merge(xleft, xright), merge(ytop, ybottom)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2157 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2158 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2159 xlab <- "Precursor Mass Discrepancy (ppm)" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2160 ylab <- "Proportion of PSMs\nin subgroup" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2161 xlim=range(data_decoy$value, na.rm = TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2162 get_ylim(boxes=boxes) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2163 if (!include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2164 xlab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2165 ylab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2166 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2167 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2168 plot(x=c(-10,10), y=c(0,1), type="n", ylim=ylim, xlim=xlim, xlab=xlab, ylab=ylab, main=main, xaxt="n", yaxt="n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2169 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2170 with(boxes, rect(xleft=xleft, xright=xright, ytop=ytop, ybottom=ybottom, lwd=scale)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2171 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2172 abline(h=1/breaks, col="blue", lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2173 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2174 get_ylim = function(boxes=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2175 is_valid_range <- function(r=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2176 return(length(r) == 2) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2177 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2178 if (! is_valid_range(ylim)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2179 ylim <<- range(c(0,boxes$ytop, boxes$ybottom)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2180 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2181 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2182 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2183 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2184 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2185 # Class: Plot_Selective_Loss |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2186 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2187 Plot_Selective_Loss = setRefClass("Plot_Selective_Loss", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2188 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2189 fields = list()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2190 Plot_Selective_Loss$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2191 initialize = function( ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2192 plot_title <<- "PMD-FDR Selectively removes Bad Hits" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2193 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2194 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2195 data_processor = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2196 return(data_processors[[1]]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2197 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2198 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2199 data_processor()$i_fdr$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2200 data_subset <- data_processor()$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2201 return(nrow(data_subset)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2202 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2203 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2204 # Support functions for plot_selective_loss() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2205 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2206 samples_lost_by_threshold <- function(updated_i_fdr=NULL, score_threshold=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2207 data_subset <- subset(updated_i_fdr, PMD_FDR_input_score >= score_threshold) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2208 tbl <- with(updated_i_fdr, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2209 table(PMD_FDR_input_score >= score_threshold, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2210 new_confidence < score_threshold, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2211 group_decoy_proteins)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2212 df <- data.frame(tbl) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2213 df_n <- aggregate(Freq~group_decoy_proteins+Var1, data=df, FUN=sum) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2214 df_n <- rename_column(df_n, name_before = "Freq", "n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2215 df <- merge(df, df_n) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2216 df$rate_of_loss <- with(df, Freq/n) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2217 df <- subset(df, (Var1==TRUE) & (Var2==TRUE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2218 df <- df[,c("group_decoy_proteins", "rate_of_loss", "n", "Freq")] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2219 if (nrow(df) > 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2220 df$score_threshold <- score_threshold |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2221 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2222 return(df) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2223 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2224 get_loss_record <- function(updated_i_fdr=NULL, score_thresholds=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2225 df=data.frame() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2226 for (score_threshold in score_thresholds){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2227 df_new_loss <- samples_lost_by_threshold(updated_i_fdr, score_threshold) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2228 df <- rbind(df, df_new_loss) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2229 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2230 return(df) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2231 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2232 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2233 # Main code for plot_selective_loss() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2234 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2235 updated_i_fdr <- data_processor()$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2236 updated_i_fdr$new_confidence <- with(updated_i_fdr, 100 * (1-i_fdr)) #ifelse((1-i_fdr) < (PMD_FDR_input_score / 100), (1-i_fdr), (PMD_FDR_input_score/100))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2237 loss_record <- get_loss_record(updated_i_fdr=updated_i_fdr, score_thresholds = 1:100) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2238 xlim <- with(loss_record, range(score_threshold)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2239 ylim <- c(0,1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2240 xlab <- "Fixed Confidence threshold (PeptideShaker score)" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2241 ylab <- "Rate of PSM disqualification from PMD-FDR" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2242 lwd <- 4 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2243 plot(x=xlim, y=ylim, type="n", main=main, xlab=xlab, ylab=ylab) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2244 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2245 groups <- sort(unique(loss_record$group_decoy_proteins)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2246 n_g <- length(groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2247 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2248 cols <- rainbow_with_fixed_intensity(n=n_g, goal_intensity_0_1 = 0.5, alpha = 1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2249 ltys <- rep(1:6, length.out=n_g) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2250 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2251 leg <- list(leg=groups, col=cols, lty=ltys, lwd=lwd, title="Species/Category") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2252 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2253 for (i in 1:n_g){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2254 lines(rate_of_loss~score_threshold, data=subset(loss_record, group_decoy_proteins==leg$leg[i]), col=leg$col[i], lwd=leg$lwd * scale, lty=leg$lty[i]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2255 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2256 abline(h=0, v=100, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2257 abline(h=c(0.1, 0.8), col="gray", lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2258 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2259 #leg = list(leg=group, col=col, lty=lty, lwd=lwd) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2260 #with(leg, legend(x = "topleft", legend = group, col = col, lty = lty, lwd = lwd, seg.len = seg.len)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2261 legend_object <- Legend_Object$new(leg, scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2262 legend_object$show() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2263 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2264 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2265 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2266 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2267 # Class: Plot_Selective_Loss_for_TOC |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2268 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2269 Plot_Selective_Loss_for_TOC = setRefClass("Plot_Selective_Loss_for_TOC", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2270 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2271 fields = list(xlab="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2272 ylab="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2273 title_x="numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2274 title_y="numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2275 legend_border="logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2276 legend_x = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2277 legend_y = "numeric", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2278 legend_title="character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2279 legend_location = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2280 name_contaminant = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2281 name_decoy = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2282 name_human = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2283 name_pyro = "character")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2284 Plot_Selective_Loss_for_TOC$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2285 initialize = function( ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2286 plot_title <<- "PMD-FDR selectively removes bad hits" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2287 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2288 xlab <<- "Confidence threshold (PeptideShaker)" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2289 ylab <<- "PMD Disqualifiction Rate" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2290 legend_border <<- FALSE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2291 #legend_title <<- "Species/Category" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2292 title_x <<- 50 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2293 title_y <<- 0.9 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2294 legend_x <<- 10 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2295 legend_y <<- 0.75 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2296 name_contaminant <<- "signal - contaminant" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2297 name_decoy <<- "decoy - reversed" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2298 name_human <<- "decoy - human" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2299 name_pyro <<- "signal - pyrococcus" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2300 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2301 data_processor = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2302 return(data_processors[[1]]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2303 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2304 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2305 data_processor()$i_fdr$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2306 data_subset <- data_processor()$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2307 return(nrow(data_subset)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2308 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2309 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2310 # Support functions for plot_selective_loss() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2311 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2312 samples_lost_by_threshold <- function(updated_i_fdr=NULL, score_threshold=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2313 data_subset <- subset(updated_i_fdr, PMD_FDR_input_score >= score_threshold) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2314 tbl <- with(updated_i_fdr, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2315 table(PMD_FDR_input_score >= score_threshold, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2316 new_confidence < score_threshold, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2317 group_decoy_proteins)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2318 df <- data.frame(tbl) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2319 df_n <- aggregate(Freq~group_decoy_proteins+Var1, data=df, FUN=sum) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2320 df_n <- rename_column(df_n, name_before = "Freq", "n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2321 df <- merge(df, df_n) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2322 df$rate_of_loss <- with(df, Freq/n) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2323 df <- subset(df, (Var1==TRUE) & (Var2==TRUE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2324 df <- df[,c("group_decoy_proteins", "rate_of_loss", "n", "Freq")] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2325 if (nrow(df) > 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2326 df$score_threshold <- score_threshold |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2327 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2328 return(df) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2329 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2330 get_loss_record <- function(updated_i_fdr=NULL, score_thresholds=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2331 df=data.frame() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2332 for (score_threshold in score_thresholds){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2333 df_new_loss <- samples_lost_by_threshold(updated_i_fdr, score_threshold) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2334 df <- rbind(df, df_new_loss) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2335 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2336 return(df) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2337 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2338 convert_groups <- function(groups=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2339 new_groups <- groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2340 new_groups <- gsub(pattern = "contaminant", replacement = name_contaminant, x = new_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2341 new_groups <- gsub(pattern = "decoy" , replacement = name_decoy , x = new_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2342 new_groups <- gsub(pattern = "human" , replacement = name_human , x = new_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2343 new_groups <- gsub(pattern = "pyrococcus" , replacement = name_pyro , x = new_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2344 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2345 return(new_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2346 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2347 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2348 # Main code for plot_selective_loss() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2349 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2350 updated_i_fdr <- data_processor()$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2351 updated_i_fdr$new_confidence <- with(updated_i_fdr, 100 * (1-i_fdr)) #ifelse((1-i_fdr) < (PMD_FDR_input_score / 100), (1-i_fdr), (PMD_FDR_input_score/100))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2352 loss_record <- get_loss_record(updated_i_fdr=updated_i_fdr, score_thresholds = 1:100) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2353 xlim <- with(loss_record, range(score_threshold)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2354 ylim <- c(0,1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2355 #xlab <- "Fixed Confidence threshold (PeptideShaker score)" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2356 #ylab <- "Rate of PSM disqualification from PMD-FDR" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2357 lwd <- 4 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2358 plot(x=xlim, y=ylim, type="n", main=main, xlab=xlab, ylab=ylab) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2359 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2360 groups <- sort(unique(loss_record$group_decoy_proteins)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2361 n_g <- length(groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2362 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2363 cols <- rainbow_with_fixed_intensity(n=n_g, goal_intensity_0_1 = 0.5, alpha = 1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2364 ltys <- rep(1:6, length.out=n_g) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2365 bty <- ifelse(legend_border, "o", "n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2366 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2367 leg <- list(leg=convert_groups(groups), var_name=groups, col=cols, lty=ltys, lwd=lwd, bty=bty, x=legend_x, y=legend_y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2368 #leg <- list(leg=groups, col=cols, lty=ltys, lwd=lwd, bty=bty, x=legend_x, y=legend_y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2369 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2370 for (i in 1:n_g){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2371 lines(rate_of_loss~score_threshold, data=subset(loss_record, group_decoy_proteins==leg$var_name[i]), col=leg$col[i], lwd=leg$lwd * scale, lty=leg$lty[i]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2372 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2373 abline(h=0, v=100, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2374 abline(h=c(0.1, 0.8), col="gray", lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2375 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2376 #leg = list(leg=group, col=col, lty=lty, lwd=lwd) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2377 #with(leg, legend(x = "topleft", legend = group, col = col, lty = lty, lwd = lwd, seg.len = seg.len)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2378 legend_object <- Legend_Object$new(leg, scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2379 legend_object$show() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2380 text(x=title_x, y=title_y, labels = plot_title) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2381 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2382 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2383 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2384 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2385 # Class: Plot_Compare_iFDR_Confidence_1_Percent_TD_FDR |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2386 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2387 Plot_Compare_iFDR_Confidence_1_Percent_TD_FDR = setRefClass("Plot_Compare_iFDR_Confidence_1_Percent_TD_FDR", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2388 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2389 fields = list()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2390 Plot_Compare_iFDR_Confidence_1_Percent_TD_FDR$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2391 initialize = function( ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2392 plot_title <<- "Precursor Mass Discrepance i-FDR for 1% Target-Decoy FDR PSMs" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2393 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2394 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2395 data_processor = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2396 return(data_processors[[1]]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2397 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2398 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2399 data_processor()$i_fdr$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2400 if (one_percent_calculation_exists()){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2401 i_fdr <- data_processor()$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2402 data_subset <- subset(i_fdr, is_in_1percent==TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2403 n <- nrow(data_subset) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2404 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2405 n <- 0 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2406 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2407 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2408 return (n) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2409 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2410 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2411 if (one_percent_calculation_exists()){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2412 i_fdr <- get_modified_fdr() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2413 report_good_discrepancies(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2414 data_TD_good <- get_data_TD_good(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2415 mean_results <- get_mean_results(data_TD_good) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2416 boxes <- mean_results |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2417 boxes <- rename_columns(df = boxes, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2418 names_before = c("min_conf", "max_conf", "lower" , "upper"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2419 names_after = c("xleft" , "xright" , "ybottom", "ytop" )) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2420 xlim <- range(boxes[,c("xleft", "xright")]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2421 ylim <- range(boxes[,c("ybottom", "ytop")]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2422 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2423 #head(mean_results) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2424 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2425 xlab = "Confidence Score (Peptide Shaker)" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2426 ylab = "Mean PMD i-FDR" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2427 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2428 if (!include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2429 xlab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2430 ylab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2431 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2432 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2433 plot(mean_i_fdr~mean_conf, data=mean_results, xlim=xlim, ylim=ylim, xlab=xlab, ylab=ylab, main=main, xaxt="n", yaxt="n", cex=scale, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2434 with(boxes, rect(xleft = xleft, ybottom = ybottom, xright = xright, ytop = ytop, lwd=scale)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2435 abline(b=-1, a=100, lwd=4*scale, col="dark gray") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2436 abline(h=0, v=100, lwd=1*scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2437 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2438 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2439 stop(sprintf("Dataset '%s' does not include 1%% FDR data", data_processor()$info$collection_name())) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2440 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2441 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2442 get_mean_results = function(data_TD_good = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2443 mean_i_fdr <- aggregate(i_fdr~conf_group, data=data_TD_good, FUN=mean) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2444 mean_i_fdr <- rename_column(mean_i_fdr, "i_fdr", "mean_i_fdr") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2445 sd_i_fdr <- aggregate(i_fdr~conf_group, data=data_TD_good, FUN=sd) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2446 sd_i_fdr <- rename_column(sd_i_fdr, "i_fdr", "sd_i_fdr") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2447 n_i_fdr <- aggregate(i_fdr~conf_group, data=data_TD_good, FUN=length) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2448 n_i_fdr <- rename_column(n_i_fdr, "i_fdr", "n") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2449 mean_conf <- aggregate(PMD_FDR_input_score~conf_group, data=data_TD_good, FUN=mean) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2450 mean_conf <- rename_column(mean_conf, "PMD_FDR_input_score", "mean_conf") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2451 min_conf <- aggregate(PMD_FDR_input_score~conf_group, data=data_TD_good, FUN=min) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2452 min_conf <- rename_column(min_conf, "PMD_FDR_input_score", "min_conf") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2453 max_conf <- aggregate(PMD_FDR_input_score~conf_group, data=data_TD_good, FUN=max) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2454 max_conf <- rename_column(max_conf, "PMD_FDR_input_score", "max_conf") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2455 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2456 mean_results <- mean_i_fdr |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2457 mean_results <- merge(mean_results, sd_i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2458 mean_results <- merge(mean_results, n_i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2459 mean_results <- merge(mean_results, mean_conf) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2460 mean_results <- merge(mean_results, min_conf) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2461 mean_results <- merge(mean_results, max_conf) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2462 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2463 mean_results$se <- with(mean_results, sd_i_fdr / sqrt(n - 1)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2464 mean_results$lower <- with(mean_results, mean_i_fdr - 2*se) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2465 mean_results$upper <- with(mean_results, mean_i_fdr + 2*se) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2466 return(mean_results) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2467 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2468 get_data_TD_good = function(i_fdr=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2469 data_TD_good <- subset(i_fdr, TD_good==TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2470 data_TD_good <- data_TD_good[order(data_TD_good$PMD_FDR_input_score),] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2471 n <- nrow(data_TD_good) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2472 data_TD_good$conf_group <- cut(1:n, breaks=floor(n/100)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2473 data_TD_good$i_fdr <- 100 * data_TD_good$i_fdr |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2474 return(data_TD_good) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2475 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2476 get_modified_fdr = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2477 i_fdr <- data_processor()$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2478 i_fdr$PMD_good <- i_fdr$i_fdr < 0.01 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2479 i_fdr$TD_good <- i_fdr$is_in_1percent == TRUE |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2480 i_fdr$conf_good <- i_fdr$PMD_FDR_input_score == 100 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2481 return(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2482 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2483 one_percent_calculation_exists = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2484 data_processor()$raw_1_percent$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2485 return(data_processor()$raw_1_percent$exists())# "is_in_1percent" %in% colnames(data_processor()$i_fdr)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2486 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2487 report_good_discrepancies = function(i_fdr=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2488 with(subset(i_fdr, (PMD_FDR_decoy == 0)), print(table(TD_good, PMD_good))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2489 with(subset(i_fdr, (PMD_FDR_input_score==100) & (PMD_FDR_decoy == 0)), print(table(TD_good, PMD_good))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2490 with(subset(i_fdr, (PMD_FDR_input_score>= 99) & (PMD_FDR_input_score<100) & (PMD_FDR_decoy == 0)), print(table(TD_good, PMD_good))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2491 with(subset(i_fdr, (PMD_FDR_input_score>= 99) & (PMD_FDR_input_score<100) & (PMD_FDR_decoy == 0)), print(table(TD_good, PMD_good))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2492 with(subset(i_fdr, (PMD_FDR_input_score>= 90) & (PMD_FDR_input_score< 99) & (PMD_FDR_decoy == 0)), print(table(TD_good, PMD_good))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2493 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2494 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2495 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2496 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2497 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2498 # Class: Plot_Density_PMD_by_Score |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2499 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2500 Plot_Density_PMD_by_Score = setRefClass("Plot_Density_PMD_by_Score", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2501 contains = "Plot_Image", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2502 fields = list(show_norm = "logical")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2503 Plot_Density_PMD_by_Score$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2504 initialize = function(p_show_norm=FALSE, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2505 show_norm <<- p_show_norm |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2506 plot_title <<- "PMD distribution, by Confidence ranges" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2507 callSuper(...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2508 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2509 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2510 data_processor = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2511 return(data_processors[[1]]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2512 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2513 get_n = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2514 return(nrow(data_processor()$data_groups$df)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2515 #data_subset <- data_collection$i_fdr |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2516 #return(nrow(data_subset)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2517 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2518 get_modified_data_groups = function(var_value = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2519 # Note: Filters out used_to_find_middle |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2520 # Note: Creates "value_of_interest" field |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2521 # Note: Remakes "group_decoy_input_score" field |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2522 data_new <- data_processor()$data_groups$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2523 data_new <- subset(data_new, !used_to_find_middle ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2524 data_new$value_of_interest <- data_new[, var_value] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2525 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2526 cutoff_points <- c(100, 100, 95, 80, 50, 0, 0) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2527 n <- length(cutoff_points) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2528 uppers <- cutoff_points[-n] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2529 lowers <- cutoff_points[-1] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2530 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2531 for (i in 1:(n-1)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2532 upper <- uppers[i] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2533 lower <- lowers[i] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2534 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2535 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2536 if (lower==upper){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2537 idx <- with(data_new, which( (PMD_FDR_input_score == upper) & (PMD_FDR_decoy == 0))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2538 cat_name <- sprintf("%d", upper) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2539 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2540 idx <- with(data_new, which((PMD_FDR_input_score >= lower) & (PMD_FDR_input_score < upper) & (PMD_FDR_decoy == 0))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2541 cat_name <- sprintf("%02d - %2d", lower, upper) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2542 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2543 data_new$group_decoy_input_score[idx] <- cat_name |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2544 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2545 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2546 return(data_new) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2547 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2548 plot_image = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2549 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2550 # Support functions for plot_density_PMD_by_score() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2551 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2552 get_densities <- function(data_subset = NULL, var_value = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2553 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2554 # Support functions for get_densities() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2555 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2556 # New version |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2557 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2558 # Main body of get_densities() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2559 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2560 data_subset <- get_modified_data_groups(var_value=var_value) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2561 #data_subset$value_of_interest <- data_subset[,var_value] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2562 from <- min(data_subset$value_of_interest, na.rm=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2563 to <- max(data_subset$value_of_interest, na.rm=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2564 xlim = range(data_subset$value_of_interest, na.rm=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2565 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2566 groups <- sort(unique(data_subset$group_decoy_input_score), decreasing = TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2567 n_groups <- length(groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2568 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2569 densities <- list(var_value = var_value, groups=groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2570 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2571 for (i in 1:n_groups){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2572 group <- groups[i] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2573 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2574 data_group_single <- subset(data_subset, (group_decoy_input_score == group)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2575 d_group <- with(data_group_single , density(value_of_interest, from = from, to = to, na.rm = TRUE)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2576 d_group <- normalize_density(d_group) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2577 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2578 densities[[group]] <- d_group |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2579 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2580 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2581 return(densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2582 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2583 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2584 get_xlim <- function(densities_a = NULL, densities_b = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2585 groups <- densities_a$groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2586 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2587 xlim <- 0 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2588 for (group in groups){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2589 xlim <- range(xlim, densities_a[[group]]$x, densities_b[[group]]$x) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2590 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2591 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2592 return(xlim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2593 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2594 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2595 get_ylim <- function(densities_a = NULL, densities_b = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2596 groups <- densities_a$groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2597 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2598 ylim <- 0 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2599 for (group in groups){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2600 ylim <- range(ylim, densities_a[[group]]$y, densities_b[[group]]$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2601 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2602 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2603 return(ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2604 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2605 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2606 plot_distributions <- function(densities = NULL, var_value= NULL,include_peak_dots=TRUE, xlab_modifier="", xlim=NULL, ylim=NULL, ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2607 data_groups <- get_modified_data_groups(var_value=var_value) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2608 groups <- sort(unique(data_groups$group_decoy_input_score)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2609 n_groups <- length(groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2610 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2611 groups_std <- setdiff(groups, c("100", "decoy", "0") ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2612 groups_std <- sort(groups_std, decreasing = TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2613 groups_std <- c(groups_std, "0") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2614 n_std <- length(groups_std) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2615 cols <- rainbow_with_fixed_intensity(n = n_std, goal_intensity_0_1 = 0.5, alpha=0.5) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2616 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2617 leg <- list(group = c("100" , groups_std , "decoy" ), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2618 leg = c("100" , groups_std , "All Decoys" ), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2619 col = c(col2hex("black") , cols , col2hex("purple", col_alpha = 0.5)), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2620 lwd = c(4 , rep(2, n_std), 4 ), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2621 title = "Confidence Score") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2622 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2623 xlab = sprintf("Precursor Mass Discrepancy%s (ppm)", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2624 xlab_modifier) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2625 ylab = "Density" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2626 if (!include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2627 xlab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2628 ylab="" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2629 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2630 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2631 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2632 plot( x=xlim, y=ylim, col=leg$col[1], lwd=leg$lwd[1] * scale, main=main, xlab=xlab, ylab=ylab, xaxt="n", yaxt="n", cex=scale, type="n")#, lty=leg.lty[1], ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2633 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2634 include_peak_dots = FALSE # BUGBUG: Disabling this for now. Need to move this to class parameter |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2635 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2636 for (i in 1:length(leg$group)){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2637 group <- leg$group[i] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2638 d <- densities[[group]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2639 lines(d, col=leg$col[i], lwd=leg$lwd[i] * scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2640 if (include_peak_dots){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2641 x=d$x[which.max(d$y)] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2642 y=max(d$y) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2643 points(x=c(x,x), y=c(0,y), pch=19, col=leg$col[i], cex=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2644 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2645 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2646 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2647 abline(v=0, lwd=scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2648 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2649 if (include_text){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2650 legend_object = Legend_Object$new(leg, scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2651 legend_object$show() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2652 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2653 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2654 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2655 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2656 # Main body for plot_density_PMD_by_score() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2657 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2658 data_groups <- data_processor()$data_groups$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2659 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2660 data_subset_a <- subset(data_groups , used_to_find_middle == FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2661 data_subset_b <- subset(data_subset_a, PMD_FDR_peptide_length > 11) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2662 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2663 densities_a <- get_densities(data_subset = data_subset_a, var_value = "value") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2664 densities_b <- get_densities(data_subset = data_subset_b, var_value = "value_norm") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2665 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2666 xlim=get_xlim(densities_a, densities_b) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2667 ylim=get_ylim(densities_a, densities_b) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2668 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2669 dataset_name <- data_processor()$info$collection_name() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2670 if (show_norm){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2671 plot_distributions(densities=densities_b, var_value = "value_norm", xlab_modifier = " - normalized", xlim=xlim, ylim=ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2672 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2673 plot_distributions(densities=densities_a, var_value = "value" , xlab_modifier = "" , xlim=xlim, ylim=ylim) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2674 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2675 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2676 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2677 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2678 # Class: Plot_Dataset_Description |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2679 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2680 Plot_Dataset_Description = setRefClass("Plot_Dataset_Description", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2681 contains = "Plot_Multiple_Images", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2682 fields = list(ylim_time_invariance = "numeric")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2683 Plot_Dataset_Description$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2684 initialize = function(p_data_processors = NULL, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2685 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2686 p_include_main=FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2687 p_ylim_time_invariance = c(-4,4), ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2688 plot_object_r1_c1 <- Plot_Time_Invariance_Alt$new(p_data_processors=p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2689 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2690 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2691 p_training_class = "good_testing", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2692 p_field_of_interest = "value", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2693 p_ylim = p_ylim_time_invariance) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2694 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2695 plot_object_r1_c2 <- Plot_Time_Invariance_Alt$new(p_data_processors=p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2696 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2697 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2698 p_training_class = "good_testing", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2699 p_field_of_interest = "value_norm", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2700 p_ylim = p_ylim_time_invariance) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2701 plot_object_r2_c1 <- Plot_Density_PMD_by_Score$new(p_data_processors=p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2702 p_show_norm=FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2703 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2704 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2705 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2706 plot_object_r2_c2 <- Plot_Density_PMD_and_Norm_Decoy_by_AA_Length$new(p_data_processors=p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2707 p_show_norm=FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2708 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2709 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2710 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2711 plot_object_r3_c1 <- Plot_Density_PMD_by_Score$new(p_data_processors=p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2712 p_show_norm=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2713 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2714 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2715 plot_object_r3_c2 <- Plot_Density_PMD_and_Norm_Decoy_by_AA_Length$new(p_data_processors=p_data_processors, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2716 p_show_norm=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2717 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2718 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2719 callSuper(p_n_images_wide=2, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2720 p_n_images_tall=3, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2721 p_include_text=p_include_text, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2722 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2723 p_image_list = list(plot_object_r1_c1, plot_object_r1_c2, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2724 plot_object_r2_c1, plot_object_r2_c2, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2725 plot_object_r3_c1, plot_object_r3_c2), ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2726 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2727 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2728 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2729 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2730 # Class: Plots_for_Paper |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2731 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2732 Plots_for_Paper <- setRefClass("Plots_for_Paper", fields =list(data_processor_a = "Data_Processor", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2733 data_processor_b = "Data_Processor", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2734 data_processor_c = "Data_Processor", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2735 data_processor_d = "Data_Processor", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2736 include_text = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2737 include_main = "logical", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2738 mai = "numeric")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2739 Plots_for_Paper$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2740 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2741 data_processor_a <<- Data_Processor$new(p_info = Data_Object_Info_737_two_step$new()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2742 data_processor_b <<- Data_Processor$new(p_info = Data_Object_Info_737_combined$new()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2743 data_processor_c <<- Data_Processor$new(p_info = Data_Object_Pyrococcus_tr $new()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2744 data_processor_d <<- Data_Processor$new(p_info = Data_Object_Mouse_Mutations $new()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2745 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2746 create_plots_for_paper = function(include_main=TRUE, finalize=TRUE){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2747 print_table_4_data() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2748 print_figure_2_data() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2749 plot_figure_D(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2750 plot_figure_C(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2751 plot_figure_B(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2752 plot_figure_A(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2753 plot_figure_8(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2754 plot_figure_7(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2755 plot_figure_6(p_scale=ifelse(finalize, 4, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2756 plot_figure_5(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2757 plot_figure_4(p_scale=ifelse(finalize, 2, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2758 plot_figure_3(p_scale=ifelse(finalize, 4, 1), p_include_main = include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2759 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2760 print_figure_2_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2761 print(create_stats_for_grouping_figure(list(data_processor_a))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2762 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2763 print_table_4_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2764 report_ranges_of_comparisons(processors = list(data_processor_a)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2765 report_ranges_of_comparisons(processors = list(data_processor_c)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2766 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2767 plot_figure_3 = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2768 plot_object <- Plot_Compare_PMD_and_Norm_Density$new(p_data_processor = list(data_processor_a), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2769 p_show_norm = FALSE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2770 p_include_text = TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2771 p_include_main = p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2772 p_display_n_psms = FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2773 plot_object$plot_image_in_small_window(p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2774 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2775 plot_figure_4 = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2776 plot_object <- Plot_Time_Invariance_Alt_Before_and_After$new(p_data_processors = list(data_processor_a), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2777 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2778 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2779 p_ylim = c(-4,4)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2780 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2781 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2782 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2783 plot_figure_5 = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2784 plot_object <- Plot_Density_PMD_and_Norm_Decoy_by_AA_Length$new(p_data_processors = list(data_processor_a), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2785 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2786 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2787 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2788 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2789 plot_figure_6 = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2790 plot_object <- Plot_Bad_CI$new(p_data_processors = list(data_processor_a), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2791 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2792 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2793 plot_object$plot_image_in_small_window(p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2794 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2795 plot_figure_7 = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2796 plot_object <- Plot_Compare_iFDR_Confidence_1_Percent_TD_FDR$new(p_data_processors = list(data_processor_a), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2797 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2798 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2799 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2800 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2801 plot_figure_8 = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2802 plot_object <- Plot_Selective_Loss$new(p_data_processors = list(data_processor_c), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2803 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2804 p_include_main=p_include_main) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2805 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2806 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2807 plot_figure_A = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2808 plot_object <- Plot_Dataset_Description$new(p_data_processors=list(data_processor_a), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2809 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2810 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2811 p_ylim_time_invariance=c(-4,4) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2812 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2813 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2814 plot_figure_B = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2815 plot_object <- Plot_Dataset_Description$new(p_data_processors=list(data_processor_b), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2816 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2817 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2818 p_ylim_time_invariance=c(-4,4) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2819 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2820 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2821 plot_figure_C = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2822 plot_object <- Plot_Dataset_Description$new(p_data_processors=list(data_processor_c), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2823 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2824 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2825 p_ylim_time_invariance=c(-4,4) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2826 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2827 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2828 plot_figure_D = function(p_scale=NULL, p_include_main=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2829 plot_object <- Plot_Dataset_Description$new(p_data_processors=list(data_processor_d), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2830 p_include_text=TRUE, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2831 p_include_main=p_include_main, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2832 p_ylim_time_invariance=c(-4,4) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2833 plot_object$plot_image_in_large_window(window_height=4, p_scale=p_scale) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2834 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2835 create_stats_for_grouping_figure = function(processors=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2836 processor <- processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2837 processor$i_fdr$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2838 aug_i_fdr <- processor$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2839 aug_i_fdr$group_good_bad_other <- gsub("_.*", "", aug_i_fdr$group_training_class) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2840 aug_i_fdr$group_null <- "all" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2841 table(aug_i_fdr$group_training_class) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2842 table(aug_i_fdr$group_good_bad_other) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2843 table(aug_i_fdr$group_null) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2844 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2845 create_agg_fdr_stats <- function(i_fdr=NULL, grouping_var_name = NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2846 formula_fdr <- as.formula(sprintf("%s~%s", "i_fdr", grouping_var_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2847 formula_len <- as.formula(sprintf("%s~%s", "PMD_FDR_peptide_length", grouping_var_name)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2848 agg_fdr <- aggregate(formula=formula_fdr, data=i_fdr, FUN=mean) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2849 agg_n <- aggregate(formula=formula_fdr, data=i_fdr, FUN=length) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2850 agg_len <- aggregate(formula=formula_len, data=i_fdr, FUN=mean) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2851 agg_fdr <- rename_columns(df = agg_fdr, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2852 names_before = c(grouping_var_name, "i_fdr"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2853 names_after = c("group" , "fdr")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2854 agg_n <- rename_columns(df = agg_n, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2855 names_before = c(grouping_var_name, "i_fdr"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2856 names_after = c("group" , "n")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2857 agg_len <- rename_columns(df = agg_len, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2858 names_before = c(grouping_var_name), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2859 names_after = c("group" )) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2860 agg <- merge(agg_fdr, agg_n) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2861 agg <- merge(agg , agg_len) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2862 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2863 return(agg) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2864 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2865 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2866 agg_detail <- create_agg_fdr_stats(i_fdr = aug_i_fdr, grouping_var_name = "group_training_class") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2867 agg_grouped <- create_agg_fdr_stats(i_fdr = aug_i_fdr, grouping_var_name = "group_good_bad_other") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2868 agg_all <- create_agg_fdr_stats(i_fdr = aug_i_fdr, grouping_var_name = "group_null") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2869 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2870 agg <- rbind(agg_detail, agg_grouped) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2871 agg <- rbind(agg, agg_all) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2872 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2873 agg$fdr <- ifelse(agg$fdr < 1, agg$fdr, 1) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2874 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2875 linear_combo <- function(x=NULL, a0=NULL, a1=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2876 result <- (a0 * (1-x) + a1 * x) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2877 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2878 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2879 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2880 agg$r <- linear_combo(agg$fdr, a0=197, a1= 47) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2881 agg$g <- linear_combo(agg$fdr, a0= 90, a1= 85) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2882 agg$b <- linear_combo(agg$fdr, a0= 17, a1=151) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2883 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2884 return(agg) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2885 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2886 report_ranges_of_comparisons = function(processors=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2887 report_comparison_of_Confidence_and_PMD = function (i_fdr = NULL, min_conf=NULL, max_conf=NULL, include_max=FALSE){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2888 report_PMD_confidence_comparison_from_subset = function(data_subset=NULL, group_name=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2889 print(group_name) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2890 print(sprintf(" Number of PSMs: %d", nrow(data_subset))) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2891 mean_confidence <- mean(data_subset$PMD_FDR_input_score) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2892 print(sprintf(" Mean Confidence Score: %3.1f", mean_confidence)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2893 print(sprintf(" PeptideShaker g-FDR: %3.1f", 100-mean_confidence)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2894 mean_PMD_FDR = mean(data_subset$i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2895 print(sprintf(" PMD g-FDR: %3.1f", 100*mean_PMD_FDR)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2896 #col <- col2hex("black", 0.2) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2897 #plot(data_subset$i_fdr, pch=".", cex=2, col=col) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2898 #abline(h=0) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2899 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2900 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2901 if (is.null(max_conf)) { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2902 data_subset <- subset(i_fdr, PMD_FDR_input_score == min_conf) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2903 group_name <- sprintf("Group %d", min_conf) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2904 } else if (include_max){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2905 data_subset <- subset(i_fdr, (PMD_FDR_input_score >= min_conf) & (PMD_FDR_input_score <= max_conf)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2906 group_name <- sprintf("Group %d through %d", min_conf, max_conf) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2907 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2908 data_subset <- subset(i_fdr, (PMD_FDR_input_score >= min_conf) & (PMD_FDR_input_score < max_conf)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2909 group_name <- sprintf("Group %d to %d", min_conf, max_conf) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2910 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2911 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2912 report_PMD_confidence_comparison_from_subset(data_subset=data_subset, group_name=group_name) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2913 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2914 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2915 processor <- processors[[1]] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2916 processor$i_fdr$ensure() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2917 i_fdr <- processor$i_fdr$df |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2918 info <- processor$info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2919 print(sprintf("PMD and Confidence comparison for -- %s", info$collection_name())) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2920 report_comparison_of_Confidence_and_PMD(i_fdr = i_fdr, min_conf=100, max_conf=NULL, include_max=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2921 report_comparison_of_Confidence_and_PMD(i_fdr = i_fdr, min_conf= 99, max_conf=100 , include_max=FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2922 report_comparison_of_Confidence_and_PMD(i_fdr = i_fdr, min_conf= 90, max_conf= 99 , include_max=FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2923 report_comparison_of_Confidence_and_PMD(i_fdr = i_fdr, min_conf= 0, max_conf=100 , include_max=TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2924 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2925 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2926 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2927 # C - 021 - PMD-FDR Wrapper - functions.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2928 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2929 # Creates the necessary structure to convert the PMD-FDR code into one that # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2930 # can run as a batch file # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2931 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2932 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2933 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2934 # Class: ModuleArgParser_PMD_FDR |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2935 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2936 ModuleArgParser_PMD_FDR <- setRefClass("ModuleArgParser_PMD_FDR", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2937 contains = c("ArgParser"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2938 fields =list(args = "character") ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2939 ModuleArgParser_PMD_FDR$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2940 initialize = function(description = "Computes individual and global FDR using Precursor Mass Discrepancy (PMD-FDR)", ...){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2941 callSuper(description=description, ...) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2942 local_add_argument("--psm_report" , help="full name and path to the PSM report") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2943 local_add_argument("--psm_report_1_percent", default = "" , help="full name and path to the PSM report for 1% FDR") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2944 local_add_argument("--output_i_fdr" , default = "" , help="full name and path to the i-FDR output file ") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2945 local_add_argument("--output_g_fdr" , default = "" , help="full name and path to the g-FDR output file ") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2946 local_add_argument("--output_densities" , default = "" , help="full name and path to the densities output file ") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2947 #local_add_argument("--score_field_name" , default = "" , help="name of score field (in R format)") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2948 local_add_argument("--input_file_type" , default = "PMD_FDR_input_file", help="type of input file (currently supports: PSM_Report)") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2949 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2950 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2951 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2952 # Class: Data_Object_Parser |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2953 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2954 Data_Object_Parser <- setRefClass("Data_Object_Parser", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2955 contains = c("Data_Object"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2956 fields =list(parser = "ModuleArgParser_PMD_FDR", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2957 args = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2958 parsing_results = "list") ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2959 Data_Object_Parser$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2960 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2961 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2962 class_name <<- "Data_Object_Parser" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2963 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2964 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2965 # Nothing to do here - parser handles verification during load |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2966 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2967 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2968 if (length(args) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2969 parsing_results <<- parser$parse_arguments(NULL) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2970 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2971 parsing_results <<- parser$parse_arguments(args) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2972 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2973 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2974 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2975 set_args = function(p_args=NULL){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2976 # This is primarily used for testing. In operation arguments will be passed automatically (through use of commandArgs) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2977 args <<- p_args |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2978 set_dirty(TRUE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2979 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2980 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2981 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2982 # Class: Data_Object_Info_Parser |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2983 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2984 Data_Object_Info_Parser <- setRefClass("Data_Object_Info_Parser", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2985 contains = c("Data_Object_Info"), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2986 fields =list( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2987 output_i_fdr = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2988 output_g_fdr = "character", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2989 output_densities = "character" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2990 ) ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2991 Data_Object_Info_Parser$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2992 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2993 callSuper() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2994 class_name <<- "Data_Object_Info_Parser" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2995 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2996 verify = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2997 check_field_exists = function(field_name=NULL, check_empty = TRUE){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2998 field_value <- get_parser()$parsing_results[field_name] |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
2999 checkTrue(! is.null(field_value), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3000 msg = sprintf("Parameter %s was not passed to PMD_FDR", field_value)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3001 if (check_empty){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3002 checkTrue(! is.null(field_value), |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3003 msg = sprintf("Parameter %s was not passed to PMD_FDR", field_value)) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3004 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3005 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3006 # Check parameters passed in |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3007 check_field_exists("junk") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3008 check_field_exists("psm_report") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3009 check_field_exists("psm_report_1_percent", check_empty = FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3010 check_field_exists("output_i_fdr" , check_empty = FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3011 check_field_exists("output_g_fdr" , check_empty = FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3012 check_field_exists("output_densities" , check_empty = FALSE) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3013 #check_field_exists("score_field_name") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3014 check_field_exists("input_file_type") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3015 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3016 m_load_data = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3017 parsing_results <- get_parser()$parsing_results |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3018 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3019 data_file_name <<- as.character(parsing_results["psm_report"]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3020 data_file_name_1_percent_FDR <<- as.character(parsing_results["psm_report_1_percent"]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3021 data_path_name <<- as.character(parsing_results[""]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3022 #experiment_name <<- data_file_name |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3023 #designation <<- "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3024 output_i_fdr <<- as.character(parsing_results["output_i_fdr"]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3025 output_g_fdr <<- as.character(parsing_results["output_g_fdr"]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3026 output_densities <<- as.character(parsing_results["output_densities"]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3027 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3028 input_file_type <<- as.character(parsing_results["input_file_type"]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3029 #score_field_name <<- as.character(parsing_results["score_field_name"]) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3030 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3031 set_parser = function(parser){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3032 parents[["parser"]] <<- parser |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3033 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3034 get_parser = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3035 return(verified_element_of_list(parents, "parser", "Data_Object_Info_Parser$parents")) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3036 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3037 file_path = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3038 result <- data_file_name # Now assumes that full path is provided |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3039 if (length(result) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3040 stop("Unable to validate file path - file name is missing") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3041 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3042 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3043 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3044 file_path_1_percent_FDR = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3045 local_file_name <- get_data_file_name_1_percent_FDR() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3046 if (length(local_file_name) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3047 result <- "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3048 } else { |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3049 result <- local_file_name # path name is no longer relevant |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3050 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3051 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3052 # Continue even if file name is missing - not all analyses have a 1 percent FDR file; this is managed downstream |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3053 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3054 # if (length(result) == 0){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3055 # stop("Unable to validate file path - one or both of path name and file name (of 1 percent FDR file) are missing") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3056 # } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3057 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3058 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3059 get_data_file_name_1_percent_FDR = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3060 return(data_file_name_1_percent_FDR) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3061 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3062 collection_name = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3063 result <- "" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3064 return(result) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3065 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3066 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3067 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3068 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3069 # Class: Processor_PMD_FDR_for_Galaxy |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3070 # Purpose: Wrapper on tools from Project 019 to enable a Galaxy-based interface |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3071 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3072 Processor_PMD_FDR_for_Galaxy <- setRefClass("Processor_PMD_FDR_for_Galaxy", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3073 fields = list( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3074 parser = "Data_Object_Parser", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3075 info = "Data_Object_Info_Parser", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3076 raw_data = "Data_Object_Raw_Data", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3077 raw_1_percent = "Data_Object_Raw_1_Percent", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3078 data_converter = "Data_Object_Data_Converter", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3079 data_groups = "Data_Object_Groupings", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3080 densities = "Data_Object_Densities", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3081 alpha = "Data_Object_Alpha", |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3082 i_fdr = "Data_Object_Individual_FDR" |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3083 )) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3084 Processor_PMD_FDR_for_Galaxy$methods( |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3085 initialize = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3086 # This initialization defines all of the dependencies between the various components |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3087 # (Unfortunately, inheriting from Data_Processor leads to issues - I had to reimplement it here with a change to "info") |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3088 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3089 # info |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3090 info$set_parser(parser) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3091 parser$append_child(info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3092 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3093 # raw_data |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3094 raw_data$set_info(info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3095 info$append_child(raw_data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3096 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3097 # raw_1_percent |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3098 raw_1_percent$set_info(info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3099 info$append_child(raw_1_percent) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3100 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3101 # data_converter |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3102 data_converter$set_info (info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3103 data_converter$set_raw_data(raw_data) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3104 info $append_child (data_converter) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3105 raw_data $append_child (data_converter) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3106 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3107 # data_groups |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3108 data_groups$set_info (info) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3109 data_groups$set_data_converter(data_converter) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3110 data_groups$set_raw_1_percent (raw_1_percent) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3111 info $append_child (data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3112 data_converter$append_child (data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3113 raw_1_percent $append_child (data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3114 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3115 # densities |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3116 densities $set_data_groups(data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3117 data_groups$append_child (densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3118 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3119 # alpha |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3120 alpha $set_densities(densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3121 densities$append_child (alpha) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3122 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3123 # i_fdr |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3124 i_fdr$set_data_groups(data_groups) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3125 i_fdr$set_densities (densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3126 i_fdr$set_alpha (alpha) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3127 data_groups $append_child(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3128 densities $append_child(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3129 alpha $append_child(i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3130 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3131 }, |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3132 compute = function(){ |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3133 #i_fdr is currently the lowest level object - it ultimately depends on everything else. |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3134 i_fdr$ensure() # All pieces on which i_fdr depends are automatically verified and computed (through their verify() and ensure()) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3135 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3136 save_standard_df(x = densities$df, file_path = info$output_densities) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3137 save_standard_df(x = alpha$df, file_path = info$output_g_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3138 save_standard_df(x = i_fdr$df, file_path = info$output_i_fdr) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3139 } |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3140 ) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3141 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3142 # D - 021 - PMD-FDR Main.R # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3143 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3144 # File Description: Contains the base code that interprets the parameters # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3145 # and computes i-FDR and g-FDR for a mass spec project # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3146 # # |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3147 ############################################################################### |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3148 argv <- commandArgs(TRUE) # Saves the parameters (command code) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3149 |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3150 processor <- Processor_PMD_FDR_for_Galaxy$new() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3151 processor$parser$set_args(argv) |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3152 processor$compute() |
5cc0c32d05a2
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
galaxyp
parents:
diff
changeset
|
3153 |