comparison scater-plot-exprs-freq.R @ 0:4887c4c69847 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author iuc
date Thu, 18 Jul 2019 11:12:33 -0400
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comparison
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-1:000000000000 0:4887c4c69847
1 #!/usr/bin/env Rscript
2
3 #Plots mean expression vs % of expressing cells and provides information as to the number of genes expressed in 50% and 25% of cells.
4 # Load optparse we need to check inputs
5
6 library(optparse)
7 library(workflowscriptscommon)
8 library(LoomExperiment)
9 library(scater)
10
11 # parse options
12
13 option_list = list(
14 make_option(
15 c("-i", "--input-loom"),
16 action = "store",
17 default = NA,
18 type = 'character',
19 help = "A SingleCellExperiment object file in Loom format."
20 ),
21 make_option(
22 c("-o", "--output-plot-file"),
23 action = "store",
24 default = NA,
25 type = 'character',
26 help = "Path of the PDF output file to save plot to."
27 )
28 )
29
30 opt <- wsc_parse_args(option_list, mandatory = c('input_loom', 'output_plot_file'))
31
32 # Check parameter values
33
34 if ( ! file.exists(opt$input_loom)){
35 stop((paste('File', opt$input_loom, 'does not exist')))
36 }
37
38
39 # Input from Loom format
40
41 scle <- import(opt$input_loom, format='loom', type='SingleCellLoomExperiment')
42
43 #produce and save the scatter plot of reads vs genes
44 plot <- plotExprsFreqVsMean(scle, controls = "is_feature_control_MT")
45 ggsave(opt$output_plot_file, plot, device="pdf")