Mercurial > repos > iuc > scater_create_qcmetric_ready_sce

annotate scater-plot-exprs-freq.R @ 1:fd808de478b1 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 14:26:31 -0400
parents 2d455a7e8a3d
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2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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1 #!/usr/bin/env Rscript
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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3 #Plots mean expression vs % of expressing cells and provides information as to the number of genes expressed in 50% and 25% of cells.
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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4 # Load optparse we need to check inputs
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2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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6 library(optparse)
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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7 library(workflowscriptscommon)
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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8 library(LoomExperiment)
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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9 library(scater)
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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11 # parse options
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12
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13 option_list = list(
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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14 make_option(
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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15 c("-i", "--input-loom"),
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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16 action = "store",
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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17 default = NA,
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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18 type = 'character',
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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19 help = "A SingleCellExperiment object file in Loom format."
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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20 ),
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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21 make_option(
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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22 c("-o", "--output-plot-file"),
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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23 action = "store",
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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24 default = NA,
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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25 type = 'character',
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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26 help = "Path of the PDF output file to save plot to."
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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27 )
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28 )
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30 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file'))
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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32 # Check parameter values
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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34 if ( ! file.exists(opt$input_loom)){
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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35 stop((paste('File', opt$input_loom, 'does not exist')))
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36 }
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39 # Input from Loom format
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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41 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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43 #produce and save the scatter plot of reads vs genes
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44 plot <- plotExprsFreqVsMean(scle, controls = "is_feature_control_MT")
2d455a7e8a3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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45 ggsave(opt$output_plot_file, plot, device="pdf")