Mercurial > repos > davidvanzessen > mutation_analysis
comparison pattern_plots.r @ 123:0453ea4d9f14 draft
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| author | davidvanzessen |
|---|---|
| date | Mon, 22 Aug 2016 07:00:23 -0400 |
| parents | |
| children | 4a93146f87aa |
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| 122:3d64b3efd352 | 123:0453ea4d9f14 |
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| 1 library(ggplot2) | |
| 2 library(reshape2) | |
| 3 | |
| 4 args <- commandArgs(trailingOnly = TRUE) | |
| 5 | |
| 6 input.file = args[1] #the data that's get turned into the "SHM overview" table in the html report "data_sum.txt" | |
| 7 plot1.file = args[2] | |
| 8 plot2.file = args[3] | |
| 9 plot3.file = args[4] | |
| 10 | |
| 11 dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T) | |
| 12 | |
| 13 classes = c("ca", "ca1", "ca2", "cg", "cg1", "cg2", "cg3", "cg4", "cm") | |
| 14 xyz = c("x", "y", "z") | |
| 15 | |
| 16 names(dat) = c("info", paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep=".")) | |
| 17 |