Mercurial > repos > miller-lab > genome_diversity
annotate population_structure.r @ 1:0df7a9b89f13
add empty snifffers section to mitigate toolshed bug; new version of dpmix
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Mon, 09 Apr 2012 12:40:57 -0400 |
| parents | 2c498d40ecde |
| children |
| rev | line source |
|---|---|
| 0 | 1 library(RColorBrewer) |
| 2 | |
| 3 args = commandArgs(trailingOnly=TRUE) | |
| 4 q_file = args[[1]] | |
| 5 output_file = args[[2]] | |
| 6 populations = args[[3]] | |
| 7 | |
| 8 tbl <- read.table(q_file) | |
| 9 | |
| 10 if ( populations >= 3 && populations <= 12 ) { | |
| 11 colors = brewer.pal(populations, 'Paired') | |
| 12 } else { | |
| 13 colors = rainbow(populations) | |
| 14 } | |
| 15 | |
| 16 pdf(file=output_file, onefile=TRUE, width=7, height=3) | |
| 17 barplot(t(as.matrix(tbl)), col=colors, xlab="Individual #", ylab="Ancestry", border=NA) | |
| 18 | |
| 19 dev.off() |