Mercurial > repos > galaxyp > cardinal_quality_report
annotate quality_report.xml @ 7:74b61bf5bc4b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
author | galaxyp |
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date | Wed, 25 Mar 2020 06:02:50 -0400 |
parents | f0d1f3e97303 |
children | bb9500286fe4 |
rev | line source |
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f0d1f3e97303
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
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1 <tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.4"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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2 <description> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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3 mass spectrometry imaging QC |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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4 </description> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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5 <macros> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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6 <import>macros.xml</import> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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7 </macros> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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8 <expand macro="requirements"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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10 <requirement type="package" version="2.3">r-gridextra</requirement> |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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11 <requirement type="package" version="3.0">r-ggplot2</requirement> |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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12 <requirement type="package" version="2.23_15">r-kernsmooth</requirement> |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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13 <requirement type="package" version="1.0.0">r-scales</requirement> |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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14 <requirement type="package" version="1.0.10"> r-pheatmap</requirement> |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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15 </expand> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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16 <command detect_errors="exit_code"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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17 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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18 @INPUT_LINKING@ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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19 cat '${cardinal_qualitycontrol_script}' && |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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20 Rscript '${cardinal_qualitycontrol_script}' |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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21 ]]> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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22 </command> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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23 <configfiles> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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24 <configfile name="cardinal_qualitycontrol_script"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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25 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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26 ################################# load libraries and read file ################# |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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27 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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28 library(Cardinal) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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29 library(ggplot2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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30 library(RColorBrewer) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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31 library(gridExtra) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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32 library(KernSmooth) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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33 library(scales) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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34 library(pheatmap) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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35 |
1
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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36 |
2
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37 @READING_MSIDATA_INRAM@ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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38 |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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39 ## remove duplicated coordinates |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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40 msidata <- msidata[,!duplicated(coord(msidata))] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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41 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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42 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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43 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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44 #if str($tabular_annotation.load_annotation) == 'yes_annotation': |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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45 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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46 ## read and extract x,y,annotation information |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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47 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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48 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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49 annotation_name = colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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50 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation" |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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51 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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52 ## merge with coordinate information of msidata |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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53 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata))) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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54 colnames(msidata_coordinates)[3] = "pixel_index" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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55 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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56 merged_annotation[is.na(merged_annotation)] = "NA" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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57 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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58 msidata\$annotation = as.factor(merged_annotation[,4]) |
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59 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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60 #end if |
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61 |
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62 ###################### calculation of data properties ################################ |
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63 @DATA_PROPERTIES_INRAM@ |
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64 |
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65 ## Median intensities |
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66 medint = round(median(spectra(msidata), na.rm=TRUE), digits=2) |
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67 ## Spectra multiplied with m/z (potential number of peaks) |
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68 numpeaks = ncol(msidata)*nrow(msidata) |
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69 ## Percentage of intensities > 0 |
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70 percpeaks = round(npeaks/numpeaks*100, digits=2) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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71 ## Number of empty TICs |
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72 TICs = colSums(spectra(msidata), na.rm=TRUE) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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73 NumemptyTIC = sum(TICs == 0) |
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74 ## Median und sd TIC |
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75 medTIC = round(median(TICs), digits=1) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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76 sdTIC = round(sd(TICs), digits=0) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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77 ## Median and sd # peaks per spectrum |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
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78 medpeaks = round(median(colSums(spectra(msidata)>0, na.rm=TRUE), na.rm=TRUE), digits=0) |
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79 sdpeaks = round(sd(colSums(spectra(msidata)>0, na.rm=TRUE), na.rm=TRUE), digits=0) |
0
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80 ## Processing informations |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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81 centroidedinfo = centroided(msidata) |
5f18275c250a
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82 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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83 ############## Read and filter tabular file with m/z ########################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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84 |
2
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85 ### reading m/z input (calibrant) file: |
0
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86 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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87 #if $calibrant_file: |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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88 |
2
d4803c1e5e19
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89 calibrant_list = read.delim("$calibrant_file", header = $calibrant_header, na.strings=c(" ","","NA"), stringsAsFactors = FALSE) |
0
5f18275c250a
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90 calibrant_list = calibrant_list[,c($mz_column, $name_column)] |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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91 |
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92 ### calculate how many input calibrant m/z are valid: |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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93 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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94 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,] |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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95 number_calibrants_in = length(calibrant_list[,1]) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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96 number_calibrants_valid = length(inputcalibrants[,1]) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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97 |
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98 #else |
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99 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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100 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2)) |
5f18275c250a
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101 number_calibrants_in = 0 |
5f18275c250a
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102 number_calibrants_valid = 0 |
5f18275c250a
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103 |
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104 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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105 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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106 ## rename input dataframe and extract m/z |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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107 colnames(inputcalibrants) = c("m/z", "name") |
5f18275c250a
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108 inputcalibrantmasses = inputcalibrants[,1] |
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109 |
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110 |
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111 ######################################## PDF ############################################# |
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112 ########################################################################################## |
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113 ########################################################################################## |
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114 |
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115 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12) |
5f18275c250a
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116 plot(0,type='n',axes=FALSE,ann=FALSE) |
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117 |
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118 ## if no filename is given, name of file in Galaxy history is used |
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119 |
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120 #if not $filename: |
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121 #set $filename = $infile.display_name |
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122 #end if |
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123 |
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124 title(main=paste("$filename")) |
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125 |
5f18275c250a
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126 ################# I) file properties in numbers ################################ |
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127 ################################################################################ |
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128 print("properties in numbers") |
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129 |
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130 properties2 = c("Median of intensities", |
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131 "Intensities > 0", |
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132 "Number of empty spectra", |
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133 "Median TIC ± sd", |
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134 "Median # peaks per spectrum ± sd", |
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135 "Centroided", |
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136 paste0("input m/z (#valid/#input) in \n", "$calibrant_file.display_name")) |
0
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137 |
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138 values2 = c(paste0(medint), |
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139 paste0(percpeaks, " %"), |
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140 paste0(NumemptyTIC), |
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141 paste0(medTIC, " ± ", sdTIC), |
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142 paste0(medpeaks, " ± ",sdpeaks), |
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143 paste0(centroidedinfo), |
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144 paste0(number_calibrants_valid, " / ", number_calibrants_in)) |
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145 |
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146 property_df2 = data.frame(properties2, values2) |
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147 colnames(property_df2) = c("properties", "values") |
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148 |
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149 property_df = rbind(property_df, property_df2) |
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150 |
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151 grid.table(property_df, rows= NULL) |
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152 |
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153 |
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154 ####################### II) x-y images ####################################### |
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155 ############################################################################## |
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156 print("x-y images") |
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157 |
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158 ## only do plots for file with intensity peaks |
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159 |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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160 if (npeaks > 0){ |
2
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161 |
0
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162 ## function for density plots |
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163 plot_colorByDensity = function(x1,x2, |
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164 ylim=c(min(x2),max(x2)), |
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165 xlim=c(min(x1),max(x1)), |
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166 xlab="",ylab="",main=""){ |
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167 df = data.frame(x1,x2) |
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168 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white"))) |
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169 df\$dens = col2rgb(x)[1,] + 1L |
5f18275c250a
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170 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256) |
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171 df\$col = cols[df\$dens] |
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172 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col, |
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173 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)} |
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174 |
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175 |
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176 ################### 0) overview for combined data ########################### |
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177 |
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178 ### only for previously combined data, same plot as in combine QC pdf |
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179 |
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180 if (!is.null(levels(msidata\$annotation))){ |
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181 |
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182 number_combined = length(levels(msidata\$annotation)) |
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183 |
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184 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation) |
5f18275c250a
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185 colnames(position_df)[3] = "annotation" |
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186 |
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187 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=annotation))+ |
5f18275c250a
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188 geom_tile() + |
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189 coord_fixed()+ |
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190 ggtitle("Spatial orientation of pixel annotations")+ |
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191 theme_bw()+ |
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192 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
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193 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+ |
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194 theme(legend.position="bottom",legend.direction="vertical")+ |
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195 guides(fill=guide_legend(ncol=4,byrow=TRUE)) |
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196 |
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197 print(combine_plot) |
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198 |
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199 ## for each annotation group find last pixel, there dashed lines will be drawn in plots over spectra index |
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200 pixel_name_df = data.frame(pixels(msidata), msidata\$annotation) |
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201 colnames(pixel_name_df) = c("pixel_number", "pixel_name") |
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202 last_pixel = aggregate(pixel_number~pixel_name, data = pixel_name_df, max) |
5f18275c250a
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203 pixel_vector = last_pixel[,2] |
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204 abline_vector = pixel_vector |
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205 |
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206 ## remove position_df to clean up RAM space |
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207 rm(position_df) |
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208 gc() |
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209 } |
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210 |
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211 ################### 1) Pixel order image ################################### |
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212 |
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213 pixelnumber = 1:pixelcount |
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214 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber) |
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215 gg_title = "Pixel order" |
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216 |
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217 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+ |
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218 geom_tile() + coord_fixed()+ |
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219 ggtitle(gg_title) + theme_bw()+ |
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220 theme(plot.title = element_text(hjust = 0.5))+ |
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221 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
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222 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), |
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223 space = "Lab", na.value = "black", name = "Pixel\nnumber")) |
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224 |
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225 ## remove pixelxyarray to clean up RAM space |
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226 rm(pixelxyarray) |
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227 gc() |
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228 |
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229 ################ 2) Number of calibrants per spectrum ###################### |
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230 |
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231 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not |
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232 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0) |
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233 |
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234 ## plot only possible when there is at least one valid calibrant |
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235 if (length(inputcalibrantmasses) != 0){ |
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236 |
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237 ## calculate plusminus values in m/z for each calibrant |
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238 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses |
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239 |
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240 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0 |
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241 |
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242 for (mass in 1:length(inputcalibrantmasses)){ |
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243 |
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244 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],] |
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245 |
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246 if (nrow(filtered_data) > 1 & sum(spectra(filtered_data),na.rm=TRUE) > 0){ |
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247 |
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248 ## intensity of all m/z > 0 |
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249 intensity_sum = colSums(spectra(filtered_data), na.rm=TRUE) > 0 |
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250 |
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251 }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data), na.rm=TRUE) > 0){ |
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252 |
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253 ## intensity of only m/z > 0 |
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254 intensity_sum = spectra(filtered_data) > 0 |
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255 |
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256 }else{ |
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257 |
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258 intensity_sum = rep(FALSE, ncol(filtered_data))} |
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259 |
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260 ## for each pixel add sum of intensities > 0 in the given m/z range |
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261 pixelmatrix = rbind(pixelmatrix, intensity_sum) |
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262 } |
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263 |
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264 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE) |
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265 countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE)) |
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266 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts |
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267 mycolours = brewer.pal(9, "Set1") |
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268 |
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269 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+ |
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270 geom_tile() + coord_fixed() + |
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271 ggtitle(paste0("Number of calibrants per pixel (±",$plusminus_ppm, " ppm)")) + |
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272 theme_bw() + |
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273 theme(plot.title = element_text(hjust = 0.5))+ |
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274 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
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275 scale_fill_manual(values = mycolours[1:length(countvector)], |
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276 na.value = "black", name = "# calibrants")) |
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277 |
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278 ## remove countdf to clean up RAM space |
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279 rm(countdf) |
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280 gc() |
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281 |
0
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282 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")} |
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283 |
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284 ########################## 3) fold change image ########################### |
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285 |
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286 #if $calibrantratio: |
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287 #for $foldchanges in $calibrantratio: |
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288 mass1 = $foldchanges.mass1 |
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289 mass2 = $foldchanges.mass2 |
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290 distance1 = $foldchanges.distance/1000000 * mass1 |
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291 distance2 = $foldchanges.distance/1000000 * mass2 |
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292 |
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293 ### if user did not write a label use input m/z as label |
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294 #if not str($foldchanges.filenameratioplot).strip(): |
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295 #set $label = "log2 fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2) |
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296 #else: |
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297 #set $label = $foldchanges.filenameratioplot |
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298 #end if |
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299 |
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300 ### filter msidata for given m/z range (for both input m/z) |
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301 filtered_data1 = msidata[mz(msidata) >= mass1-distance1 & mz(msidata) <= mass1+distance1,] |
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302 filtered_data2 = msidata[mz(msidata) >= mass2-distance2 & mz(msidata) <= mass2+distance2,] |
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303 ### m/z range for each plot (fixed range of 5 Da) |
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304 ### xlim does not work because it does not adjust for the max. intensities within the range |
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305 mzdown1 = features(msidata, mz = mass1-2) |
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306 mzup1 = features(msidata, mz = mass1+3) |
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307 mzdown2 = features(msidata, mz = mass2-2) |
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308 mzup2 = features(msidata, mz = mass2+3) |
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309 |
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310 ### plot for first m/z |
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311 par(mfrow=c(2,1), oma=c(0,0,2,0)) |
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312 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("Average spectrum ", mass1, " Da")) |
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313 abline(v=c(mass1-distance1, mass1, mass1+distance1), col="blue",lty=c(3,6,3)) |
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314 |
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315 ### plot for second m/z |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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316 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("Average spectrum ", mass2, " Da")) |
2
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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317 abline(v=c(mass2-distance2, mass2, mass2+distance2), col="blue", lty=c(3,6,3)) |
0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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318 title("Control of fold change plot", outer=TRUE) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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changeset
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319 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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320 ### filter spectra for max m/z to have two vectors, which can be divided |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
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321 ### plot spatial distribution of fold change |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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322 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
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323 ## calculate mean intensity for each m/z over the ppm range; then calculate log2 foldchange |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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324 mass1vector = colMeans(spectra(filtered_data1), na.rm =TRUE) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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325 mass2vector = colMeans(spectra(filtered_data2), na.rm = TRUE) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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326 foldchange= log2(mass1vector/mass2vector) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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327 fcmatrix = cbind(foldchange, coord(msidata)[,1:2]) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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328 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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329 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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330 geom_tile() + coord_fixed()+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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331 ggtitle("$label")+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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332 theme_bw()+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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333 theme(plot.title = element_text(hjust = 0.5))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
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334 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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335 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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336 ,space = "Lab", na.value = "black", name ="FC")) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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337 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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338 ## remove FC files to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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339 rm(fcmatrix) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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340 rm(filtered_data1) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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341 rm(filtered_data2) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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342 gc() |
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343 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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344 #end for |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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345 #end if |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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346 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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347 #################### 4) m/z heatmaps ####################################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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348 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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349 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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350 if (length(inputcalibrants[,1]) != 0){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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351 for (mass in 1:length(inputcalibrants[,1])){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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352 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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353 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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354 image(msidata, mz=inputcalibrants[,1][mass], plusminus=plusminusvalues[mass], |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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355 main= paste0(inputcalibrants[,2][mass], ": ", round(inputcalibrants[,1][mass], digits = 2)," (±",$plusminus_ppm, " ppm)"), |
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356 contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-1)) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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357 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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358 } else {print("4) The input peptide and calibrant m/z were not provided or outside the m/z range")} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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359 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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360 #################### 5) Number of peaks per pixel - image ################## |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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361 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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362 ## here every intensity value > 0 counts as peak |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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363 peaksperpixel = colSums(spectra(msidata)> 0, na.rm=TRUE) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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364 peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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365 |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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366 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel))+ |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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367 geom_tile() + coord_fixed() + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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368 ggtitle("Number of peaks per spectrum")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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369 theme_bw() + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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370 theme(plot.title = element_text(hjust = 0.5))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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371 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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372 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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373 ,space = "Lab", na.value = "black", name = "# peaks")) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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374 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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375 ## remove peakscoordarray to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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376 rm(peakscoordarray) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
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377 gc() |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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378 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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379 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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380 ############################### 6) TIC image ############################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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381 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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382 TICcoordarray=cbind(coord(msidata)[,1:2], TICs) |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
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383 |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
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384 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs))+ |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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385 geom_tile() + coord_fixed() + |
5
f0d1f3e97303
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
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386 ggtitle("Total Ion Current")+ |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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387 theme_bw() + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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388 theme(plot.title = element_text(hjust = 0.5))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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389 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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390 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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391 ,space = "Lab", na.value = "black", name = "TIC")) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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changeset
|
392 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
393 ## remove TICcoordarray to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
394 rm(TICcoordarray) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
395 gc() |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
396 |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
397 ############################### 6b) median int image ############################### |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
398 |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
399 median_int = apply(spectra(msidata),2,median) |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
400 median_coordarray=cbind(coord(msidata)[,1:2], median_int) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
401 |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
402 print(ggplot(median_coordarray, aes(x=x, y=y, fill=median_int))+ |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
403 geom_tile() + coord_fixed() + |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
404 ggtitle("Median intensity per spectrum")+ |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
405 theme_bw() + |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
406 theme(plot.title = element_text(hjust = 0.5))+ |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
407 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
408 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
409 ,space = "Lab", na.value = "black", name = "median\nintensity")) |
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
410 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
411 ## remove median_coordarray to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
412 rm(median_coordarray) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
413 gc() |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
414 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
415 ############################### 6c) max int image ############################### |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
416 |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
417 max_int = apply(spectra(msidata),2,max) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
418 max_coordarray=cbind(coord(msidata)[,1:2], max_int) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
419 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
420 print(ggplot(max_coordarray, aes(x=x, y=y, fill=max_int))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
421 geom_tile() + coord_fixed() + |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
422 ggtitle("Maximum intensity per spectrum")+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
423 theme_bw() + |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
424 theme(plot.title = element_text(hjust = 0.5))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
425 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
426 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
427 ,space = "Lab", na.value = "black", name = "max\nintensity")) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
428 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
429 ## remove median_coordarray to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
430 rm(max_coordarray) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
431 gc() |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
432 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
433 ############################### 7) Most abundant m/z image ################# |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
434 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
435 ## for each spectrum find the row (m/z) with the highest intensity |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
436 highestmz = apply(spectra(msidata),2,which.max) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
437 ## in case for some spectra max returns integer(0), highestmz is a list and integer(0) have to be replaced with NA and unlisted |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
438 if (class(highestmz) == "list"){ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
439 ##find zero-length values |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
440 zero_entry <- !(sapply(highestmz, length)) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
441 ### replace these values with NA |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
442 highestmz[zero_entry] <- NA |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
443 ### unlist list to get a vector |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
444 highestmz = unlist(highestmz)} |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
445 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
446 highestmz_matrix = cbind(coord(msidata)[,1:2],mz(msidata)[highestmz]) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
447 colnames(highestmz_matrix)[3] = "highestmzinDa" |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
448 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
449 print(ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
450 geom_tile() + coord_fixed() + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
451 ggtitle("Most abundant m/z in each spectrum")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
452 theme_bw() + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
453 theme(plot.title = element_text(hjust = 0.5))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
454 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z", |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
455 limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
456 theme(text=element_text(family="ArialMT", face="bold", size=12))) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
457 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
458 ## remove highestmz_matrix to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
459 rm(highestmz_matrix) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
460 gc() |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
461 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
462 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
463 ########################## 8) optional pca image for two components ################# |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
464 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
465 #if $do_pca: |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
466 |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
467 set.seed(1) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
468 pca = PCA(msidata, ncomp=2) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
469 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
470 ## plot overview image and plot and PC1 and 2 images |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
471 par(mfrow = c(2,1)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
472 plot(pca, col=c("black", "darkgrey"), main="PCA for two components") |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
473 image(pca, col=c("black", "white"), strip=FALSE, ylim= c(maximumy+0.2*maximumy,minimumy-1)) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
474 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
475 for (PCs in 1:2){ |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
476 print(image(pca, column = c(paste0("PC",PCs)) , strip=FALSE, superpose = FALSE, main=paste0("PC", PCs), col.regions = risk.colors(100), ylim=c(maximumy+2, minimumy-2)))} |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
477 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
478 ## remove pca to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
479 rm(pca) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
480 gc() |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
481 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
482 #end if |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
483 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
484 ################## III) properties over spectra index ###################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
485 ############################################################################ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
486 print("properties over pixels") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
487 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
488 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
489 ########################## 9) number of peaks per spectrum ################# |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
490 ## 9a) scatterplot |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
491 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
492 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
493 title(xlab="Spectra index", line=3) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
494 title(ylab="Number of peaks", line=4) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
495 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
496 if (!is.null(levels(msidata\$annotation))){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
497 abline(v=abline_vector, lty = 3)} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
498 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
499 ## 9b) histogram |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
500 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
501 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
502 title(main="Number of peaks per spectrum", line=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
503 title(ylab="Frequency = # spectra", line=4) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
504 abline(v=median(peaksperpixel), col="blue") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
505 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
506 ## 9c) additional histogram to show contribution of annotation groups |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
507 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
508 if (!is.null(levels(msidata\$annotation))){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
509 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
510 df_9 = data.frame(peaksperpixel, msidata\$annotation) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
511 colnames(df_9) = c("Npeaks", "annotation") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
512 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
513 hist_9 = ggplot(df_9, aes(x=Npeaks, fill=annotation)) + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
514 geom_histogram()+ theme_bw()+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
515 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
516 theme(plot.title = element_text(hjust = 0.5))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
517 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
518 theme(legend.position="bottom",legend.direction="vertical")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
519 labs(title="Number of peaks per spectrum and annotation group", x="Number of peaks per spectrum", y = "Frequency = # spectra") + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
520 guides(fill=guide_legend(ncol=5,byrow=TRUE))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
521 geom_vline(xintercept = median(peaksperpixel), size = 1, colour = "black",linetype = "dashed") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
522 print(hist_9)} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
523 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
524 ########################## 10) TIC per spectrum ########################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
525 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
526 ## 10a)density scatterplot |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
527 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
528 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
529 ## colorDensityplot does not work after TIC normalization, therefore make normal plot |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
530 if (min(TICs) == max(TICs)){ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
531 plot(pixels(msidata), TICs, ylab = "", xlab = "", pch=20, main="TIC per spectrum", col="#FF3100") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
532 }else{ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
533 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
534 } |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
535 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
536 title(xlab="Spectra index", line=3) |
5
f0d1f3e97303
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents:
4
diff
changeset
|
537 title(ylab = "Total ion current intensity", line=4) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
538 if (!is.null(levels(msidata\$annotation))){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
539 abline(v=abline_vector, lty = 3)} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
540 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
541 ## 10b) histogram |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
542 hist((TICs), main="", las=1, xlab = "TIC per spectrum", ylab="") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
543 title(main= "TIC per spectrum", line=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
544 title(ylab="Frequency = # spectra", line=4) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
545 abline(v=median(TICs[TICs>0]), col="blue") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
546 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
547 ## 10c) additional histogram to show annotation contributions |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
548 if (!is.null(levels(msidata\$annotation))){ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
549 df_10 = data.frame((TICs), msidata\$annotation) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
550 colnames(df_10) = c("TICs", "annotation") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
551 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
552 hist_10 = ggplot(df_10, aes(x=TICs, fill=annotation)) + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
553 geom_histogram()+ theme_bw()+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
554 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
555 theme(plot.title = element_text(hjust = 0.5))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
556 theme(legend.position="bottom",legend.direction="vertical")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
557 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
558 labs(title="TIC per spectrum and annotation group", x="TIC per spectrum", y = "Frequency = # spectra") + |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
559 guides(fill=guide_legend(ncol=5,byrow=TRUE))+ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
560 geom_vline(xintercept = median(TICs[TICs>0]), size = 1, colour = "black",linetype = "dashed") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
561 print(hist_10)} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
562 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
563 ################################## IV) properties over m/z #################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
564 ############################################################################ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
565 print("properties over m/z") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
566 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
567 ########################## 11) Histogram of m/z values ##################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
568 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
569 par(mfrow = c(1, 1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
570 hist(mz(msidata), xlab = "m/z", main="Histogram of m/z values") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
571 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
572 ########################## 12) Number of peaks per m/z ##################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
573 |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
574 peakspermz = rowSums(spectra(msidata) > 0, na.rm=TRUE) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
575 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
576 par(mfrow = c(2,1), mar=c(5,6,4,4.5)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
577 ## 12a) scatterplot |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
578 plot_colorByDensity(mz(msidata),peakspermz, main= "Number of peaks per m/z", ylab ="") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
579 title(xlab="m/z", line=2.5) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
580 title(ylab = "Number of peaks", line=4) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
581 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
582 mtext("Coverage of spectra [%]", 4, line=3, adj=1) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
583 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
584 ## 12b) histogram |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
585 hist(peakspermz, main="", las=1, ylab="", xlab="") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
586 title(ylab = "Frequency", line=4) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
587 title(main="Number of peaks per m/z", xlab = "Number of peaks per m/z", line=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
588 abline(v=median(peakspermz), col="blue") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
589 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
590 ########################## 13) Sum of intensities per m/z ################## |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
591 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
592 ## Sum of all intensities for each m/z (like TIC, but for m/z instead of pixel) |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
593 mzTIC = rowSums(spectra(msidata), na.rm=TRUE) ## calculate intensity sum for each m/z |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
594 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
595 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
596 ## 13a) scatterplot |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
597 plot_colorByDensity(mz(msidata),mzTIC, main= "Sum of intensities per m/z", ylab ="") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
598 title(xlab="m/z", line=2.5) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
599 title(ylab="Intensity sum", line=4) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
600 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
601 ## 13b) histogram |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
602 hist(mzTIC, main="", xlab = "", las=1, ylab="") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
603 title(main="Sum of intensities per m/z", line=2, ylab="") |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
604 title(xlab = "sum of intensities per m/z") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
605 title(ylab = "Frequency", line=4) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
606 abline(v=median(mzTIC[mzTIC>0]), col="blue") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
607 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
608 ################################## V) intensity plots ######################## |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
609 ############################################################################ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
610 print("intensity plots") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
611 ########################## 14) Intensity distribution ###################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
612 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
613 par(mfrow = c(2,1), mar=c(5,6,4,2)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
614 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
615 ## 14a) Median intensity over spectra |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
616 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
617 medianint_spectra = apply(spectra(msidata), 2, median, na.rm=TRUE) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
618 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index", ylab="") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
619 title(ylab="Median spectrum intensity", line=4) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
620 if (!is.null(levels(msidata\$annotation))){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
621 abline(v=abline_vector, lty = 3)} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
622 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
623 ## 14b) histogram: |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
624 hist(spectra(msidata), main="", xlab = "", ylab="", las=1) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
625 title(main="Intensity histogram", line=2) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
626 title(xlab="intensities") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
627 title(ylab="Frequency", line=4) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
628 abline(v=median(spectra(msidata)[(spectra(msidata)>0)], na.rm=TRUE), col="blue") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
629 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
630 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
631 ## 14c) histogram to show contribution of annotation groups |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
632 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
633 if (!is.null(levels(msidata\$annotation))){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
634 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
635 df_13 = data.frame(matrix(,ncol=2, nrow=0)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
636 for (subsample in levels(msidata\$annotation)){ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
637 log2_int_subsample = spectra(msidata)[,msidata\$annotation==subsample] |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
638 df_subsample = data.frame(as.numeric(log2_int_subsample)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
639 df_subsample\$annotation = subsample |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
640 df_13 = rbind(df_13, df_subsample)} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
641 df_13\$annotation = as.factor(df_13\$annotation) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
642 colnames(df_13) = c("int", "annotation") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
643 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
644 hist_13 = ggplot(df_13, aes(x=int, fill=annotation)) + |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
645 geom_histogram()+ theme_bw()+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
646 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
647 labs(title="Intensities per sample", x="intensities", y = "Frequency") + |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
648 theme(plot.title = element_text(hjust = 0.5))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
649 theme(legend.position="bottom",legend.direction="vertical")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
650 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
651 guides(fill=guide_legend(ncol=5,byrow=TRUE))+ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
652 geom_vline(xintercept = median(spectra(msidata)[(spectra(msidata)>0)]), size = 1, colour = "black",linetype = "dashed") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
653 print(hist_13) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
654 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
655 ## 14d) boxplots to visualize in a different way the intensity distributions |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
656 par(mfrow = c(1,1), cex.axis=1.3, cex.lab=1.3, mar=c(13.1,4.1,5.1,2.1)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
657 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
658 mean_matrix = matrix(,ncol=0, nrow = nrow(msidata)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
659 for (subsample in levels(msidata\$annotation)){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
660 mean_mz_sample = rowMeans(spectra(msidata)[,msidata\$annotation==subsample],na.rm=TRUE) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
661 mean_matrix = cbind(mean_matrix, mean_mz_sample)} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
662 |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
663 boxplot(log10(mean_matrix), ylab = "Log10 mean intensity per m/z", main="Log10 mean m/z intensities per annotation group", xaxt = "n") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
664 (axis(1, at = c(1:number_combined), labels=levels(msidata\$annotation), las=2)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
665 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
666 ## 14e) Heatmap of pearson correlation on mean intensities between annotation groups |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
667 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
668 corr_matrix = mean_matrix |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
669 corr_matrix[corr_matrix == 0] <- NA |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
670 colnames(corr_matrix) = levels(msidata\$annotation) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
671 ## pearson correlation is only possible if there are at least 2 groups |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
672 if (length(colnames)>1) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
673 { |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
674 corr_matrix = cor(corr_matrix, method= "pearson",use="complete.obs") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
675 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
676 heatmap.parameters <- list(corr_matrix, |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
677 show_rownames = T, show_colnames = T, |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
678 main = "Pearson correlation on mean intensities") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
679 do.call("pheatmap", heatmap.parameters) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
680 } |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
681 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
682 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
683 ################################## VI) Mass spectra and m/z accuracy ######################## |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
684 ############################################################################ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
685 print("Mass spectra and m/z accuracy") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
686 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
687 ############################ 15) Mass spectra ############################## |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
688 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
689 ## replace any NA with 0, otherwise plot function will not work at all |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
690 msidata_no_NA = msidata |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
691 spectra(msidata_no_NA)[is.na(spectra(msidata_no_NA))] = 0 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
692 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
693 ## find three equal m/z ranges for the average mass spectra plots: |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
694 third_mz_range = nrow(msidata_no_NA)/3 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
695 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
696 par(mfrow = c(2, 2), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
697 plot(msidata_no_NA, pixel = 1:ncol(msidata_no_NA), main= "Average spectrum") |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
698 plot(msidata_no_NA[1:third_mz_range,], pixel = 1:ncol(msidata_no_NA), main= "Zoomed average spectrum") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
699 plot(msidata_no_NA[third_mz_range:(2*third_mz_range),], pixel = 1:ncol(msidata_no_NA), main= "Zoomed average spectrum") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
700 plot(msidata_no_NA[(2*third_mz_range):nrow(msidata_no_NA),], pixel = 1:ncol(msidata_no_NA), main= "Zoomed average spectrum") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
701 |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
702 ## plot one average mass spectrum for each pixel annotation group |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
703 |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
704 if (!is.null(levels(msidata\$annotation))){ |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
705 ## print legend only for less than 10 samples |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
706 if (length(levels(msidata\$annotation)) < 10){ |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
707 key_legend = TRUE |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
708 }else{key_legend = FALSE} |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
709 par(mfrow = c(1,1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1)) |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
710 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE, main="Average mass spectra for annotation groups") |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
711 } |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
712 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
713 ## plot 4 random mass spectra |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
714 ## find four random pixel to plot their spectra in the following plots: |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
715 pixel1 = sample(pixelnumber,1) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
716 pixel2 = sample(pixelnumber,1) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
717 pixel3 = sample(pixelnumber,1) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
718 pixel4 = sample(pixelnumber,1) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
719 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
720 par(mfrow = c(2, 2), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1)) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
721 plot(msidata_no_NA, pixel = pixel1, main=paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel1,1:2]))) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
722 plot(msidata_no_NA, pixel = pixel2, main=paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel2,1:2]))) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
723 plot(msidata_no_NA, pixel = pixel3, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel3,1:2]))) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
724 plot(msidata_no_NA, pixel = pixel4, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel4,1:2]))) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
725 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
726 ################### 16) Zoomed in mass spectra for calibrants ############## |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
727 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
728 count = 1 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
729 differencevector = numeric() |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
730 differencevector2 = vector() |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
731 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
732 if (length(inputcalibrantmasses) != 0){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
733 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
734 ### calculate plusminus values in m/z for each calibrant, this is used for all following plots |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
735 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses)) * inputcalibrantmasses |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
736 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
737 for (mass in 1:length(inputcalibrantmasses)){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
738 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
739 ### define the plot window with xmin und xmax |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
740 minmasspixel1 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-0.5) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
741 maxmasspixel1 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+1.5) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
742 minmasspixel2 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-0.25) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
743 maxmasspixel2 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+0.5) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
744 minmasspixel3 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-3) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
745 maxmasspixel3 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+3) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
746 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
747 ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
748 filtered_data = msidata_no_NA[mz(msidata_no_NA) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata_no_NA) <= inputcalibrantmasses[mass]+plusminusvalues[mass],] |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
749 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
750 if (nrow(filtered_data) > 0 & sum(spectra(filtered_data)) > 0){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
751 maxmassrow = rowMeans(spectra(filtered_data)) ## for each m/z average intensity is calculated |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
752 maxvalue = mz(filtered_data)[which.max(maxmassrow)] ### m/z with highest average intensity in m/z range |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
753 mzdifference = maxvalue - inputcalibrantmasses[mass] ### difference: theoretical value - closest m/z value |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
754 ppmdifference = mzdifference/inputcalibrantmasses[mass]*1000000 ### calculate ppm for accuracy measurement |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
755 }else{ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
756 ppmdifference = NA |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
757 maxvalue = NA} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
758 differencevector[mass] = round(ppmdifference, digits=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
759 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
760 ### find m/z closest to inputcalibrant and calculate ppm difference for plot 18 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
761 mznumber = features(msidata_no_NA, mz = inputcalibrantmasses[mass]) ### gives featurenumber which is closest to given m/z |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
762 mzvalue = mz(msidata_no_NA)[mznumber] ### gives closest m/z |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
763 mzdifference2 = mzvalue - inputcalibrantmasses[mass] |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
764 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
765 differencevector2[mass] = round(ppmdifference2, digits=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
766 |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
767 ## plotting of 4 spectra in one page |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
768 par(mfrow = c(2, 2), oma=c(0,0,2,0)) |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
769 ## average plot |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
770 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel = 1:length(pixelnumber), main= "Average spectrum") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
771 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
772 abline(v=c(maxvalue), col="red", lty=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
773 abline(v=c(mzvalue), col="green2", lty=4) |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
774 ## average plot including points per data point |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
775 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel = 1:length(pixelnumber), main="Average spectrum with data points") |
5
f0d1f3e97303
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents:
4
diff
changeset
|
776 points(mz(msidata_no_NA[minmasspixel1:maxmasspixel1,]), rowMeans(spectra(msidata_no_NA)[minmasspixel1:maxmasspixel1,,drop=FALSE]), col="blue", pch=20) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
777 ## plot of third average plot |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
778 plot(msidata_no_NA[minmasspixel2:maxmasspixel2,], pixel = 1:length(pixelnumber), main= "Average spectrum") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
779 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
780 abline(v=c(maxvalue), col="red", lty=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
781 abline(v=c(mzvalue), col="green2", lty=4) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
782 ## plot of fourth average plot |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
783 plot(msidata_no_NA[minmasspixel3:maxmasspixel3,], pixel = 1:length(pixelnumber), main= "Average spectrum") |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
784 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
785 abline(v=c(maxvalue), col="red", lty=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
786 abline(v=c(mzvalue), col="green2", lty=4) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
787 title(paste0("theor. m/z: ", round(inputcalibrants[count,1], digits=4)), col.main="blue", outer=TRUE, line=0, adj=0.074) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
788 title(paste0("most abundant m/z: ", round(maxvalue, digits=4)), col.main="red", outer=TRUE, line=0, adj=0.49) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
789 title(paste0("closest m/z: ", round(mzvalue, digits=4)), col.main="green2", outer=TRUE, line=0, adj=0.93) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
790 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
791 ### 16b) one large extra plot with different colours for different pixel annotation groups |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
792 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
793 if (!is.null(levels(msidata\$annotation))){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
794 if (number_combined < 10){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
795 key_zoomed = TRUE |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
796 }else{key_zoomed = FALSE} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
797 par(mfrow = c(1, 1)) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
798 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel=1:ncol(msidata_no_NA),main="Average spectrum per annotation group", |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
799 pixel.groups=msidata\$annotation, key=key_zoomed, col=hue_pal()(number_combined),superpose=TRUE) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
800 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="black", lty=c(3,1,3)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
801 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
802 count=count+1 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
803 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
804 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
805 ## remove msidata_no_NA to clean up RAM space |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
806 rm(msidata_no_NA) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
807 gc() |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
808 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
809 ######### 17) ppm difference input calibrant m/z and m/z with max intensity in given m/z range######### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
810 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
811 par(mfrow = c(1,1)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
812 ### plot the ppm difference calculated above: theor. m/z value to highest m/z value: |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
813 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
814 calibrant_names = as.character(inputcalibrants[,2]) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
815 diff_df = data.frame(differencevector, calibrant_names) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
816 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
817 if (sum(is.na(diff_df[,1])) == nrow(diff_df)){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
818 plot(0,type='n',axes=FALSE,ann=FALSE) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
819 title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range")) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
820 }else{ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
821 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
822 diff_plot1=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
823 labs(title="Average m/z error (max. average intensity vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
824 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
825 geom_text(aes(label=differencevector), vjust=-0.3, size=5.5, col="blue") + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
826 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
827 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
828 print(diff_plot1) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
829 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
830 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
831 ######### 18) ppm difference input calibrant m/z and closest m/z ########### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
832 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
833 ### plot the ppm difference calculated above theor. m/z value to closest m/z value: |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
834 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
835 differencevector2 = round(differencevector2, digits=2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
836 calibrant_names = as.character(inputcalibrants[,2]) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
837 diff_df = data.frame(differencevector2, calibrant_names) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
838 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
839 diff_plot2=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector2)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() + |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
840 labs(title="Average m/z error (closest measured m/z vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
841 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
842 geom_text(aes(label=differencevector2), vjust=-0.3, size=5.5, col="blue")+ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
843 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
844 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
845 print(diff_plot2) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
846 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
847 #################### 19) ppm difference over pixels ##################### |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
848 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
849 par(mfrow = c(1,1)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
850 count = 1 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
851 ppm_df = as.data.frame(matrix(,ncol=0, nrow = ncol(msidata))) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
852 for (calibrant in inputcalibrantmasses){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
853 ### find m/z with the highest mean intensity in m/z range, if no m/z in the range, ppm differences for this calibrant will be NA |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
854 filtered_data = msidata[mz(msidata) >= calibrant-plusminusvalues[count] & mz(msidata) <= calibrant+plusminusvalues[count],] |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
855 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
856 if (nrow(filtered_data) > 0){ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
857 ### filtered for m/z range, find max peak in each spectrum |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
858 ppm_vector = numeric() |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
859 for (pixel_count in 1:ncol(filtered_data)){ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
860 ## for each spectrum (pixel_count) find the m/z that has the highest intensity |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
861 mz_max = mz(filtered_data)[which.max(spectra(filtered_data)[,pixel_count])] |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
862 mzdiff = mz_max - calibrant |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
863 ppmdiff = mzdiff/calibrant*1000000 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
864 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
865 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot) |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
866 if (max(spectra(filtered_data)[,pixel_count]) == 0 || is.na(max(spectra(filtered_data)[,pixel_count]))){ |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
867 ppmdiff = NA} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
868 ppm_vector[pixel_count] = ppmdiff} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
869 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
870 }else{ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
871 ppm_vector = rep(NA, ncol(msidata)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
872 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
873 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
874 ppm_df = cbind(ppm_df, ppm_vector) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
875 count=count+1 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
876 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
877 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
878 if (sum(is.na(ppm_df)) == ncol(ppm_df)*nrow(ppm_df)){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
879 plot(0,type='n',axes=FALSE,ann=FALSE) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
880 title(main=paste("plot 19: no peaks in the chosen region, repeat with higher ppm range")) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
881 }else{ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
882 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
883 ### plot ppm differences over pixels (spectra index) |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
884 par(mar=c(4.1, 4.1, 4.1, 8.5)) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
885 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
886 plot(0,0,type="n", ylim=c(min(ppm_df, na.rm=TRUE),max(ppm_df, na.rm=TRUE)), xlim = c(1,ncol(filtered_data)),xlab = "Spectra index", ylab = "m/z difference in ppm", main="Difference m/z with max. average intensity vs. theor. m/z\n(per spectrum)") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
887 for (each_cal in 1:ncol(ppm_df)){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
888 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")} |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
889 legend("topright", inset=c(-0.2,0), xpd = TRUE, bty="n", cex=0.8,legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1) |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
890 if (!is.null(levels(msidata\$annotation))){ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
891 abline(v=abline_vector, lty = 3)}} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
892 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
893 ### make x-y-images for mz accuracy |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
894 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
895 ppm_dataframe = cbind(coord(msidata)[,1:2], ppm_df) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
896 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
897 for (each_cal in 1:ncol(ppm_df)){ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
898 tmp_ppm = ppm_dataframe[,c(1,2,each_cal+2)] |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
899 tmp_ppm[,3] = as.numeric(tmp_ppm[,3]) |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
900 colnames(tmp_ppm) = c("x","y", "ppm_each_cal") |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
901 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
902 print(ggplot(tmp_ppm, aes(x=x, y=y, fill=ppm_each_cal))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
903 geom_tile() + coord_fixed() + |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
904 ggtitle(paste0("m/z accuracy for ",inputcalibrants[,2][each_cal]))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
905 theme_bw() + |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
906 theme(plot.title = element_text(hjust = 0.5))+ |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
907 theme(text=element_text(family="ArialMT", face="bold", size=12))+ |
3
16556ca0196b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents:
2
diff
changeset
|
908 scale_fill_gradient2(low = "navy", mid = "grey", high = "red", midpoint = 0 ,space = "Lab", na.value = "black", name = "ppm\nerror"))} |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
909 |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
910 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
911 }else{print("plot 16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")} |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
912 }else{ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
913 print("inputfile has no intensities > 0") |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
914 } |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
915 dev.off() |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
916 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
917 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
918 ]]></configfile> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
919 </configfiles> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
920 <inputs> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
921 <expand macro="reading_msidata"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
922 <conditional name="tabular_annotation"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
923 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for QC plots"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
924 <option value="no_annotation" selected="True">pixels belong into one group only</option> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
925 <option value="yes_annotation">use pixel annotation from a tabular file</option> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
926 </param> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
927 <when value="yes_annotation"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
928 <expand macro="reading_pixel_annotations"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
929 </when> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
930 <when value="no_annotation"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
931 </conditional> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
932 <expand macro="pdf_filename"/> |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
933 <expand macro="reading_2_column_mz_tabular" optional="true"/> |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
934 <param name="plusminus_ppm" value="200" type="float" label="ppm range" help="Will be added in both directions to input calibrant m/z"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
935 <param name="do_pca" type="boolean" label="PCA with 2 components"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
936 <repeat name="calibrantratio" title="Plot fold change of two m/z" min="0" max="10"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
937 <param name="mass1" value="1111" type="float" label="M/z 1" help="First m/z"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
938 <param name="mass2" value="2222" type="float" label="M/z 2" help="Second m/z"/> |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
939 <param name="distance" value="200" type="float" label="ppm range" help="Will be added in both directions to input calibrant m/z and intensities will be averaged in this range."/> |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
940 <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
941 <sanitizer invalid_char=""> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
942 <valid initial="string.ascii_letters,string.digits"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
943 <add value="_" /> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
944 </valid> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
945 </sanitizer> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
946 </param> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
947 </repeat> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
948 </inputs> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
949 <outputs> |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
950 <data format="pdf" name="QC_report" from_work_dir="qualitycontrol.pdf" label = "${tool.name} on ${on_string}: results"/> |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
951 </outputs> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
952 <tests> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
953 <test> |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
954 <param name="infile" value="" ftype="imzml"> |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
955 <composite_data value="Example_Processed.imzML"/> |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
956 <composite_data value="Example_Processed.ibd"/> |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
957 </param> |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
958 <conditional name="processed_cond"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
959 <param name="processed_file" value="processed"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
960 <param name="accuracy" value="200"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
961 <param name="units" value="ppm"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
962 </conditional> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
963 <conditional name="tabular_annotation"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
964 <param name="load_annotation" value="no_annotation"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
965 </conditional> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
966 <param name="calibrant_file" value="inputcalibrantfile1.tabular" ftype="tabular"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
967 <param name="mz_column" value="1"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
968 <param name="name_column" value="1"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
969 <param name="plusminus_ppm" value="100"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
970 <param name="filename" value="Testfile_imzml"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
971 <param name="do_pca" value="True"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
972 <repeat name="calibrantratio"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
973 <param name="mass1" value="328.9"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
974 <param name="mass2" value="398.8"/> |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
975 <param name="distance" value="500"/> |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
976 <param name="filenameratioplot" value = "Ratio of mass1 (328.9) / mass2 (398.8)"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
977 </repeat> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
978 <output name="QC_report" file="QC_imzml.pdf" compare="sim_size"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
979 </test> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
980 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
981 <test> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
982 <expand macro="infile_analyze75"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
983 <conditional name="tabular_annotation"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
984 <param name="load_annotation" value="no_annotation"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
985 </conditional> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
986 <param name="filename" value="Testfile_analyze75"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
987 <param name="do_pca" value="True"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
988 <output name="QC_report" file="QC_analyze75.pdf" compare="sim_size"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
989 </test> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
990 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
991 <test> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
992 <param name="infile" value="3_files_combined.RData" ftype="rdata"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
993 <conditional name="tabular_annotation"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
994 <param name="load_annotation" value="yes_annotation"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
995 <param name="annotation_file" value="annotations_rdata.tabular"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
996 <param name="column_x" value="1"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
997 <param name="column_y" value="2"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
998 <param name="column_names" value="3"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
999 <param name="tabular_header" value="True"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1000 </conditional> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1001 <param name="calibrant_file" value="inputcalibrantfile1.tabular" ftype="tabular"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1002 <param name="mz_column" value="1"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1003 <param name="name_column" value="1"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1004 <param name="plusminus_ppm" value="100"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1005 <param name="filename" value="Testfile_rdata"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1006 <param name="do_pca" value="True"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1007 <output name="QC_report" file="QC_rdata.pdf" compare="sim_size"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1008 </test> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1009 <test> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1010 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1011 <conditional name="tabular_annotation"> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1012 <param name="load_annotation" value="no_annotation"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1013 </conditional> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1014 <param name="calibrant_file" value="inputcalibrantfile2.txt"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1015 <param name="mz_column" value="1"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1016 <param name="name_column" value="2"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1017 <param name="filename" value="Testfile_rdata"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1018 <param name="do_pca" value="False"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1019 <output name="QC_report" file="QC_empty_spectra.pdf" compare="sim_size"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1020 </test> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1021 </tests> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1022 <help> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1023 <![CDATA[ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1024 @CARDINAL_DESCRIPTION@ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1025 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1026 ----- |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1027 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1028 This tool uses Cardinal to read files and create a quality control report with descriptive plots for mass spectrometry imaging data. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1029 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1030 @MSIDATA_INPUT_DESCRIPTION@ |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1031 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1032 @SPECTRA_TABULAR_INPUT_DESCRIPTION@ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1033 - at least two different annotations should be in the annotation column |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1034 |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1035 @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@ |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1036 - maximum of 9 m/z values per run are supported |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1037 - names should be unique |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1038 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1039 **Options** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1040 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1041 - m/z of interest (e.g. internal calibrants) and the ppm range are used for m/z heatmaps (x-y grid), heatmap of number of calibrants per spectrum (x-y grid), zoomed in mass spectra, m/z accuracy plots |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1042 - Optional fold change plot: draws a heatmap (x-y grid) for the fold change of two m/z (log2(intensity ratio)) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1043 - All plots are described in more detail below |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1044 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1045 **Tip** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1046 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1047 - For additional m/z heatmaps use the MSI mz images tool and to plot more mass spectra use the MSI mass spectra tool. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1048 - To obtain the underlaying spectra and feature values used in this quality report, the imzML exporter tool can be used |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1049 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1050 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1051 **Output** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1052 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1053 - quality control report as pdf with key numbers and descriptive plots describing the mass spectrometry imaging data |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1054 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1055 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1056 ---------------------------------------------------------------------------------------------------------------------------------------------------- |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1057 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1058 **Overview of the QC report plots** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1059 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1060 - (annot): this plots will only be drawn if pixel annotations are loaded via a tabular file |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1061 - (cal): this plots will only be drawn if a tabular file with at least one valid calibrant m/z is provided |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1062 - (FC): this plots will only be drawn if the optional fold change image is selected |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1063 - Vertical lines in histograms represent median values. In density scatter plots the colour changes from blue to green, yellow and red the more points are overlayed. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1064 |
5
f0d1f3e97303
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents:
4
diff
changeset
|
1065 - Overview of file properties: Numbers and ranges for m/z features and pixels are given. Median and range across all intensity values are provided. Intensities > 0 gives the percentage of m/z-pixel pairs with an intensity above zero. The number of empty spectra (TIC = 0), the median number of peaks (intensities > 0) per spectra as well as the median TIC (total ion current) are given. The processing status of the file is provided as well as the number of valid calibrants from the provided tabular file.> 0 (Intensities > 0). |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1066 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1067 **x-y images (pixel/spectra information)** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1068 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1069 - (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1070 - Pixel order: Shows the order of the pixels in the provided file. Depending on the instrument this can represent the acquisition order. If annotation file is provided pixels are ordered according to annotation groups. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1071 - (cal) Number of calibrants per pixel: In every spectrum the calibrant m/z window (calibrant m/z plusminus 'ppm range') is searched for peaks (intensity > 0). Calibrants are considered present in a spectrum when they have at least one peak in their m/z window. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1072 - (FC) Control of fold change plot: For both input m/z a zoomed in average spectrum is drawn with the input m/z as blue dashed line, the m/z range as blue dotted lines and the maximum intensity in the m/z window with a red line. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1073 - (FC) Fold change image: For each input m/z the average intensity within the given ppm range is calculated, then the log2 fold change of both average intensities is taken and plotted as heatmap. |
3
16556ca0196b
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents:
2
diff
changeset
|
1074 - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z (can be outside the ppm range). The intensities are averaged within the calibrant m/z window (ppm range). |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1075 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap. |
5
f0d1f3e97303
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents:
4
diff
changeset
|
1076 - Total ion current: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap. |
1
ae9ffc7ba261
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents:
0
diff
changeset
|
1077 - Median intensity: For each spectrum the median intensity is plotted as heatmap. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1078 - Maximum intensity: For each spectrum the maximum intensity is plotted as heatmap. |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1079 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1080 - PCA for two components: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels, principal components 1 and 2 are also plotted as x-y image. |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1081 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1082 **Properties over spectra/pixels** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1083 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1084 - Number of peaks per spectrum: Scatter plot and histogram showing the number of intensities > 0 for each spectrum. If annotation tabular file is provided, the pixels are sorted according to annotation groups and the dotted lines in the scatter plot separate spectra of different annotation groups. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1085 - (annot) Number of peaks per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1086 - TIC per spectrum: Scatter plot and histogram showing the sum of all intensities per spectrum (TIC). Dotted lines in the scatter plot separate spectra of different annotation groups. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1087 - (annot) TIC per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group. Only the length of the coloured bar is important and not its height from zero, as bars are added up and not overlayed. |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1088 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1089 **Properties over m/z features** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1090 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1091 - Histogram of m/z values: Histogram of all m/z values (complete m/z axis) |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1092 - Number of peaks per m/z: Scatter plot and histogram giving the number of intensities > 0 for each m/z. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1093 - Sum of intensities per m/z: Scatter plot and histogram of the sum of all intensities per m/z. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1094 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1095 **Intensity plots** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1096 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1097 - Median intensity per spectrum: Scatter plot in which each point represents the median intensity for one spectrum. Dotted lines in the scatter plot separate spectra of different annotation groups. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1098 - Histogram of intensities. |
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1099 - (annot) Intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group. |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
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1100 - (annot) Log10 mean intensities per m/z and annotation group: For all pixels of an annotation group the log10 mean intensity for each m/z is calculated and shown as boxplot. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1101 - (annot) Pearson correlation between annotation groups (needs at least 2 groups) based on mean intensities and shown as heatmap. |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1102 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1103 **Mass spectra and m/z accuracy** |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1104 |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
|
1105 - Average mass spectra: First plot shows the average spectrum over the full m/z range, the other three plots zoom into the m/z axis. |
4
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
1106 - (annot) Average mass spectrum per annotation group. |
3b7a35d50ebf
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents:
3
diff
changeset
|
1107 - Random mass spectra: The mass spectra for four random pixel are plotted. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
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1108 - (cal) For each calibrant four zoomed average mass spectrum are drawn with different zooming level. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window. In the second spectrum each blue dot indicates one data point. |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1109 - (annot) Average spectrum per annotation group: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each annotation group separately. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1110 - (cal) Difference m/z with max. average intensity vs. theor. calibrant m/z: The difference in ppm between the m/z with the highest average intensity and the theoretical m/z are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the red line in the zoomed in mass spectra. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1111 - (cal) Difference closest measured m/z vs. theor. calibrant m/z: The difference in ppm between the closest m/z value and the theoretical m/z values are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the green line in the zoomed in mass spectra. |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1112 - (cal) Difference m/z with max. average intensity vs. theor. m/z (per spectrum): For each spectrum the ppm difference between the m/z with the highest average intensity and the theoretical m/z are plotted. The calibrants have different plotting colours. Dashed lines separate spectra of different annotation groups. |
2
d4803c1e5e19
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents:
1
diff
changeset
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1113 - (cal) Same m/z accuracy in ppm is plotted per calibrant and per spectrum as image in x-y dimension. |
0
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1114 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1115 |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1116 ]]> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1117 </help> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1118 <expand macro="citations"/> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
|
1119 </tool> |
5f18275c250a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff
changeset
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1120 |