Mercurial > repos > iuc > scater_plot_tsne

annotate scater-plot-pca.R @ 0:a30f4bfe8f01 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 14:30:21 -0400
parents
children 2b09ca1c5e41
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a30f4bfe8f01 "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
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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2
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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3 # Creates a PCA plot of a normalised SingleCellExperiment object.
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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4
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5 # Load optparse we need to check inputs
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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6
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7 library(optparse)
a30f4bfe8f01 "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)
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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11
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12 # parse options
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13
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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14 option_list = list(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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15 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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16 c("-i", "--input-loom"),
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17 action = "store",
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18 default = NA,
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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19 type = 'character',
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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20 help = "A SingleCellExperiment object file in Loom format."
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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21 ),
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22 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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23 c("-c", "--colour-by"),
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24 action = "store",
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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25 default = NULL,
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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26 type = 'character',
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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27 help = "Feature (from annotation file) to colour PCA plot points by. The values represented in this options should be categorical"
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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28 ),
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29 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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30 c("-s", "--size-by"),
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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31 action = "store",
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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32 default = NULL,
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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33 type = 'character',
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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34 help = "Feature (from annotation file) to size PCA plot points by. The values represented in this options should be numerical and not categorical"
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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35 ),
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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36 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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37 c("-p", "--shape-by"),
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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38 action = "store",
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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39 default = NULL,
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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40 type = 'character',
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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41 help = "Feature (from annotation file) to shape PCA plot points by. The values represented in this options should be categorical"
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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42 ),
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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43 make_option(
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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44 c("-o", "--output-plot-file"),
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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45 action = "store",
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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46 default = NA,
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47 type = 'character',
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48 help = "Path of the PDF output file to save plot to."
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49 )
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50 )
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51
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52 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file'))
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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53 # Check parameter values
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54
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55 if ( ! file.exists(opt$input_loom)){
a30f4bfe8f01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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56 stop((paste('File', opt$input_loom, 'does not exist')))
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57 }
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58
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59
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60 # Input from Loom format
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61
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62 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
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63 scle <- normalize(scle, exprs_values = 1)
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64 scle <- runPCA(scle)
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65 plot <- plotReducedDim(scle, "PCA", colour_by = opt$colour_by, size_by = opt$size_by, shape_by = opt$shape_by)
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66 #do the scatter plot of reads vs genes
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67
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68 ggsave(opt$output_plot_file, plot, device="pdf")