Mercurial > repos > iuc > scater_filter

annotate scater-plot-tsne.R @ 1:b7ea9f09c02f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author iuc
date Tue, 03 Sep 2019 14:27:39 -0400
parents
children 7a365ec81b52
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b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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1 #!/usr/bin/env Rscript
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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2
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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3 # Creates a t-SNE plot of a normalised SingleCellExperiment object.
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4
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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5 # Load optparse we need to check inputs
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6
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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7 library(optparse)
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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8 library(workflowscriptscommon)
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9 library(LoomExperiment)
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10 library(scater)
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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11 library(Rtsne)
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12
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13 # parse options
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14
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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15 option_list = list(
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16 make_option(
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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17 c("-i", "--input-loom"),
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18 action = "store",
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19 default = NA,
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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20 type = 'character',
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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21 help = "A SingleCellExperiment object file in Loom format."
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22 ),
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23 make_option(
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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24 c("-c", "--colour-by"),
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25 action = "store",
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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26 default = NULL,
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27 type = 'character',
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28 help = "Feature (from annotation file) to colour t-SNE plot points by. The values represented in this options should be categorical"
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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29 ),
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30 make_option(
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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31 c("-s", "--size-by"),
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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32 action = "store",
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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33 default = NULL,
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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34 type = 'character',
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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35 help = "Feature (from annotation file) to size t-SNE plot points by. The values represented in this options should be numerical and not categorical"
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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36 ),
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37 make_option(
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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38 c("-p", "--shape-by"),
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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39 action = "store",
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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40 default = NULL,
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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41 type = 'character',
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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42 help = "Feature (from annotation file) to shape t-SNE plot points by. The values represented in this options should be categorical"
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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43 ),
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44 make_option(
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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45 c("-o", "--output-plot-file"),
b7ea9f09c02f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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46 action = "store",
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47 default = NA,
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48 type = 'character',
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49 help = "Path of the PDF output file to save plot to."
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50 )
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51 )
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52
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53 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file'))
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54 # Check parameter values
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55
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56 if ( ! file.exists(opt$input_loom)){
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57 stop((paste('File', opt$input_loom, 'does not exist')))
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58 }
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59
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60
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61 # Input from Loom format
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62
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63 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
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64 scle <- normalize(scle, exprs_values = 1)
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65 scle <- runTSNE(scle, perplexity=10)
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66 plot <- plotTSNE(scle, colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by)
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67
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68
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69 ggsave(opt$output_plot_file, plot, device="pdf")