Oxford_Grid_Vespula_pensylvanica.R

Vpen_ox<-read.table(file.choose(), header=T)
plot(Vpen_ox$full_LM~Vpen_ox$full_pos, pch='.', xlim=c(0, 179008480), ylim=c(0, 3120))
abline(v=19704315)
abline(v=38559230)
abline(v=50757430)
abline(v=61054492)
abline(v=70252996)
abline(v=79155476)
abline(v=87886121)
abline(v=96418841)
abline(v=104790567)
abline(v=113120597)
abline(v=120503542)
abline(v=126001468)
abline(v=131102752)
abline(v=136180405)
abline(v=141114780)
abline(v=145998127)
abline(v=150181423)
abline(v=154329963)
abline(v=158241185)
abline(v=162096999)
abline(v=165940011)
abline(v=169718080)
abline(v=173222578)
abline(v=176566496)
abline(v=179008480)
abline(h=315.823)
abline(h=613.415)
abline(h=826.678)
abline(h=1020.375)
abline(h=1238.119)
abline(h=1379.237)
abline(h=1558.762)
abline(h=1691.026)
abline(h=1825.989)
abline(h=1958.833)
abline(h=2073.308)
abline(h=2189.297)
abline(h=2286.838)
abline(h=2377.536)
abline(h=2465.869)
abline(h=2535.515)
abline(h=2613.986)
abline(h=2673.278)
abline(h=2723.984)
abline(h=2796.282)
abline(h=2853.303)
abline(h=2922.775)
abline(h=2998.547)
abline(h=3067.732)
abline(h=3120)
abline(v=0, h=0)

# generating a QQ plot for GWAS data
pvals<-read.table(file.choose(), header=T)
library(lattice)
qqmath(~-log10(pvals$p_wald), distribution=function(x){-log10(qunif(1-x))})