Two scripts to plot BLINK results using rMVP

makeSummaryTable.py

# assuming that all results tables of BLINK are in the current folder, and assuming that all results tables were gzipped
# usage: python makeSummaryTable.py > Summary_Table.tsv

# this script will make one large summary table in the format rMVP requires, SNP, chrom, position, and then x columns for x phenotypes - each cell one p-value
# use grep -v to kick out regions of the genome you don't want to plot (unplaced contigs etc.)

import glob
import gzip
from collections import OrderedDict
all_phenos = ['SNP','chr','pos']
snp_dict = OrderedDict()
for x in glob.glob('*txt.gz'):
    pheno = x.replace('_GWAS_result.txt.gz','')
    all_phenos.append(pheno)
    with gzip.open(x, 'rb') as fh:
        for line in fh:
            ll = line.split()
            if ll[0] == 'taxa': continue
            #['1_1', '1', '1', '7.228916e-02', '1.882767e-01']
            snp = ll[0]
            if snp in snp_dict:
                snp_dict[snp].append(ll[-1])
            else:
                snp_dict[snp] = [ll[-1]]

print('\t'.join(all_phenos))
for s in snp_dict:
    snp_name = s
    ss = s.split('_')
    snp_chrom = ss[0]
    snp_pos = ss[1]
    thisll = [snp_chrom, snp_pos, str(int(snp_pos)+2)]
    thisll = '\t'.join(thisll) + "\t" + snp_name+'_'+ '_'.join(snp_dict[s])
    print(thisll)

plotMVP.R

library(readr)
library(rMVP)
# this script can easily run for a few hours
df <- read_tsv('Summary_Table.tsv')
# make x Manhattan plots for x phenotypes - for journal submission it's probably better to use file='tiff'

MVP.Report(df, plot.type="m", LOG10=TRUE, ylim=NULL, threshold=c(1e-6,1e-4),threshold.lty=c(1,2),
            col=c("dodgerblue4","deepskyblue"), threshold.lwd=c(1,1), threshold.col=c("black","grey"), amplify=TRUE,
            chr.den.col=c("darkgreen", "yellow", "red"),bin.size=1e6,signal.col=c("red","green"),
            signal.cex=c(1,1),signal.pch=c(19,19),file="jpg",memo="",dpi=300)

# make x QQ-plots for x phenotypes
MVP.Report(df,plot.type="q",conf.int.col=NULL,box=TRUE,file="jpg",memo="",dpi=300)