-
Notifications
You must be signed in to change notification settings - Fork 0
/
plot_sbs_script.R
60 lines (52 loc) · 1.96 KB
/
plot_sbs_script.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
#!/usr/bin/Rscript
###########################################################################
###########################################################################
# Code to plot unstranded SBS (single base substitution) spectra and signatures
#
# 2018 09 14
#
# v0.1
#
# An alpha version
#
# Copyright (C) 2018 Steven G. Rozen and Mi Ni Huang
#
# The code is released under GPL-3
# https://www.gnu.org/licenses/gpl-3.0.en.html
# you can redistribute it and/or modify it under the terms of the
# GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option)
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# Contact: steverozen@gmail.com
###########################################################################
###########################################################################
## input: indel.catalog.csv
args = commandArgs(trailingOnly=TRUE)
inputfile = args[1]
source("plot_sbs.R")
## plot the unstranded SBS catalogs
plot_snvs_file(inputfile)
### for Jaegil's sigs combined plot
if (FALSE){
inputfile = '~/Desktop/ICGC-upload/Mutation_Signatures/approach_2/SignatureAnalyzer_COMPOSITE_SBS_W96.signature.csv'
data <- read.csv(inputfile)
outputfile2 <- gsub('csv', 'combined.pdf', inputfile)
cairo_pdf(outputfile2, width=11.6929, height=9.2677, onefile=T)
par(mfrow=c(15,4), mar=c(0.3,0.1,0.3,0.1), oma=c(2,2,2,0))
for (i in 3:6){
plot_snvs(data[,i], colnames(data)[i], classes='top', grid.line=F)
}
for (i in 7:58){
plot_snvs(data[,i], colnames(data)[i], classes=F, grid.line=F)
}
for (i in 59:62){
plot_snvs(data[,i], colnames(data)[i], classes='bottom', grid.line=F)
}
invisible(dev.off())
}