Mercurial > repos > iuc > scater_plot_dist_scatter
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 |
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date | Thu, 18 Jul 2019 11:12:33 -0400 |
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-1:000000000000 | 0:4887c4c69847 |
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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") |