Plot genome-wide association study analysis summary statsitics, label genes at hits of interest and in general try to make some pretty pictures.
This is a repository to help make plots similar to Figure 2 in https://www.biorxiv.org/content/10.1101/388165v3
...but maybe with less skyscrapers (maybe more, who knows?).
Rscript manhattanPlotter.R [gwas] [hits] [output]
[gwas] <-- a file containing GWAS summary statistics. Mandatory columns to include are SNP, CHR, BP and P.
In this file SNP is a unique text identifier for the variant of interest, CHR is the chromosome number, BP is the base pair position and P is the p-value for the SNP parameter.
[hits] <-- a file containing annotation for GWAS hits of interest. Mandatory columns to include are SNP, STATUS and GENE.
In this file, SNPs of interest are listed with a STATUS indicator (binary) and a GENE label (character strings).
[output]<-- a character string with no spaces, whatever you want to name this plot.
Pretty straightforward.
GWAS file
SNP CHR BP P
chr1:60320992 1 60320992 0.38
chr8:135908647 8 135908647 0.66
chr11:97895884 11 97895884 0.31
chr18:814730 18 814730 0.91
chr10:120407145 10 120407145 0.12
chr11:29372878 11 29372878 0.82
chr3:164053059 3 164053059 0.21
chr20:14479321 20 14479321 0.20
chr2:220200263 2 220200263 0.31
...
Hits file
SNP STATUS GENE
chr1:154898185 0 PMVK
chr1:155135036 0 KRTCAP2
chr1:155205634 0 GBAP1
chr1:161469054 1 FCGR2A
chr1:171719769 1 VAMP4
chr1:205723572 0 NUCKS1
chr1:205737739 0 RAB29
chr1:226916078 0 ITPKB
chr1:232664611 0 SIPA1L2
...
Command
Rscript manhattanPlotter.R testGwas.tab testHits.tab testPlot
R > 3.5 with packages data.table, tidyverse, ggrepel and reshape2
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