How to plot SNPs distribution on each chromosome?

Question

[Yuyayuya]

Hello everyone!

I want to visualize SNPs results of progeny compared with two parents in the whole genome (to see the introgression regions). For example, plot all the chromosome of progeny and show what regions are from which parent on each chromosome. I guess it should like the figure attached.

Is there any package or software recommend?

*I tried SEG-Map but I got an empty pseudo-reference sequence.

[lakhujanivijay]

You can try karyoploteR

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotMarkers/PlotMarkers.html

Answer 1

[Alex Reynolds]

Maybe this will help get you started.

Here's a script to simulate input:

#!/usr/bin/env python

import sys
from random import randint

chrs = ['chr1',
        'chr2',
        'chr3',
        'chr4',
        'chr5',
        'chr6',
        'chr7',
        'chr8',
        'chr9',
        'chr10',
        'chr11',
        'chr12',
        'chr13',
        'chr14',
        'chr15',
        'chr16',
        'chr17',
        'chr18',
        'chr19',
        'chr20',
        'chr21',
        'chr22',
        'chrX',
        'chrY']

bounds = [248956422,
          242193529,
          198295559,
          190214555,
          181538259,
          170805979,
          159345973,
          145138636,
          138394717,
          133797422,
          135086622,
          133275309,
          114364328,
          107043718,
          101991189,
          90338345,
          83257441,
          80373285,
          58617616,
          64444167,
          46709983,
          50818468,
          156040895,
          57227415]

binsize = 1000000
maxmutations = 100

for chri,chrv in enumerate(chrs):
    bound = bounds[chri]
    chr = chrv
    for start in range(0, bound, binsize):
        mutations = randint(0, maxmutations)
        sys.stdout.write('%s\t%d\t%d\t.\t%d\n' % (chr, start, start + binsize, mutations))

You might run it like so, to get some test input:

$ ./simulateMutations.py | sort-bed - > mutations.bed

Then you could plot it with something like the following:

#!/usr/bin/env Rscript

suppressPackageStartupMessages(require(optparse))

option_list = list(
  make_option(c("-i", "--input"), action="store", default=NA, type='character', help="input filename"),
  make_option(c("-o", "--output"), action="store", default=NA, type='character', help="output filename")
)
opt = parse_args(OptionParser(option_list=option_list))

d <- read.table(opt$input, header=F, stringsAsFactor=T, col.names=c("chr", "start", "stop", "id", "mutations"))
d$chr <- factor(d$chr, levels = c('chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY'))
d <- with(d, d[order(chr),])

library(ggplot2)
pdf(opt$output)

p <- ggplot(data=d, aes(x=start, y=1)) +
  facet_grid(chr ~ ., switch='y') +
  geom_tile(aes(fill=mutations)) +
  theme(axis.title.y=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank(),
        strip.text.y = element_text(angle = 180)) +
  scale_fill_gradientn(colours = rainbow(5), breaks=seq(min(d$mutations),max(d$mutations),(max(d$mutations)-min(d$mutations))/4))

print(p)
dev.off()

You might run it like so:

$ ./plotMutations.Rscript -i mutations.bed -o mutations.pdf

This will make a figure that looks like this:

Pretty close to what you want, but not exact. You could use Stack Overflow and other resources to tweak the ggplot2 code to do what you need for your particular dataset: change axis and panel labels, sort order, color gradient, breaks, etc.

Once you have a sense of how the input looks and how the script works, you could use fetchChromSizes from UCSC Kent utilties and bedops, bedmap and vcf2bed from BEDOPS to measure counts of real SNPs-of-interest over bins:

$ fetchChromSizes hg38 | awk '{ print $1"\t0\t"$2; }' | sort-bed - > hg38.bed
$ bedmap --echo --count --delim '\t' <(bedops --split 1000000 hg38.bed) <(vcf2bed < snps.vcf) > snp_counts_over_bins.bed

From that you could measure percentages or density over bins:

$ MAXCOUNT=`cut -f4 snp_counts_over_bins.bed | sort -nr | head -1`
$ awk -vmax=${MAXCOUNT} '{ $4=($4*100)/max; print $0; }' snp_counts_over_bins.bed > snp_perc_over_bins.bed

You could use snp_perc_over_bins.bed as the input to the aforementioned R script.