Post date: Nov 15, 2016 3:54:3 AM
I used the R packages qtl and wgaim to plot the scaffold linkage map to include as a figure for the genome admixture paper. Files for this are in ~/projects/lyc_hybanc/map. Here is what I did:
1. Used R to sort the linkage map
2. Used perl to make a 'data file' with phenotype and genotype data. This is simply required for reading in the actual map and is not part of the plot.
perl mkmm.pl 1258 sortedMap.txt
3. Plot the map in R (here is the code):
library(qtl)
library(wgaim)
map<-read.cross("mm",".","mm.txt","sortedMap.txt")
pdf("map.pdf",width=12,height=6)
link.map(map,cex=0.2,m.cex=0.3,cex.lab=1.3)
dev.off()