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11. Publication Plotting.R
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##### PLOTTING CoxPH and GLM GWAS #####
##### GAMMA == BLUE (#1F78B4(.122, .471, .706), #419fde(.255, .624, .871)) #####
##### HZE == RED (#DB2B3D (.859, .169, .239), #e66c79(.902, .424, .475)) #####
##### ALL.IRR == Purple (#663399 (.4, .2, .6), #8c53c6 (.549, .325, .776)) #####
##### UNIRRADIATED == GREEN (#33A02C (.2, .627, .173), #53ce4b (.325, .808 ,.294)) #####
library(GenomicRanges)
library(BSgenome.Mmusculus.UCSC.mm10)
library(DOQTL)
library(HZE)
par(mfrow = c(5,1), mar=c(1, 4, 1, 1) + 0.5)
#layout(matrix(4:1, 4, 1))
plot.hs.color.qtl(hze, bin.width = 100, color = "red", main = "HZE ion irradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(gamma, bin.width = 100, color = "blue", main = "Gamma-ray irradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(allirr, bin.width = 100, color = "purple", main = "All Irradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(un, bin.width = 100, color = "green", main = "Unirradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(all, bin.width = 100, color = "black", main = "All mice", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
par(mfrow = c(5,1), mar=c(1, 4, 1, 1) + 0.5)
#layout(matrix(4:1, 4, 1))
plot.hs.color.qtl(hze[15], bin.width = 10, color = "red", main = "HZE ion irradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(gamma[15], bin.width = 10, color = "blue", main = "Gamma-ray irradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(allirr[15], bin.width = 10, color = "purple", main = "All Irradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(un[15], bin.width = 10, color = "green", main = "Unirradiated", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl(all[15], bin.width = 10, color = "black", main = "All mice", ylim = c(0, 9.5))
abline(a = 5.73, b = 0, col = "grey")
#abline(a = 4.48, b = 0, col = "lightgrey")
plot.hs.color.qtl = function(qtl, bin.width = 1000, color = "black", ...) {
new.qtl = NULL
for(chr in 1:length(qtl)) {
library(BSgenome.Mmusculus.UCSC.mm10)
print(chr)
# Create 100 SNP bins.
brks = cut(x = 1:length(qtl[[chr]]), breaks = length(qtl[[chr]]) / bin.width)
# Split up the SNP positions and get the mean.
pos = split(start(qtl[[chr]]), brks)
pos = sapply(pos, mean)
# Split up the p-values and get the max.
pv = split(mcols(qtl[[chr]])$p.value, brks)
pv = sapply(pv, min)
# Make a single new GRanges object to return.
gr = GRanges(seqnames = seqnames(qtl[[chr]])[1],
ranges = IRanges(start = pos, width = 1), p.value = pv)
if(chr == 1) {
new.qtl = gr
} else {
new.qtl = c(new.qtl, gr)
} # else
} # for(chr)
# Get the chromosome lengths.
chrlen = seqlengths(BSgenome.Mmusculus.UCSC.mm10)
names(chrlen) = sub("^chr", "", names(chrlen))
chrlen = chrlen[seqlevels(new.qtl)] * 1e-6
# Add the chr lengths to the chromosomes for plotting.
# Switch positions to genome Mb.
gmb = start(new.qtl) * 1e-6
for(chr in 2:length(chrlen)) {
wh = which(seqnames(new.qtl) == names(chrlen)[chr])
gmb[wh] = gmb[wh] + sum(chrlen[1:(chr - 1)])
} # for(chr)
# Get chromosome mid-points for plotting the Chr name.
chrmid = (chrlen / 2) + cumsum(c(1, chrlen[-length(chrlen)]))
# Make the plot.
if(color == "purple") {
col = rep(rgb(.4, .2, .6), length(new.qtl))
even.chr = which(seqnames(new.qtl) %in% (1:10 * 2))
col[even.chr] = rgb(.549, .325, .776)
plot(gmb, -log10(new.qtl$p.value), pch = 20, xaxt = "n",
col = col, las = 1, xlab = "", ylab = "-log10(p-value)", ...)
mtext(side = 1, line = 0.5, at = chrmid, text = names(chrlen), cex = 1.2)
}
if(color == "red") {
col = rep(rgb(.859, .169, .239), length(new.qtl))
even.chr = which(seqnames(new.qtl) %in% (1:10 * 2))
col[even.chr] = rgb(.902, .424, .475)
plot(gmb, -log10(new.qtl$p.value), pch = 20, xaxt = "n",
col = col, las = 1, xlab = "", ylab = "-log10(p-value)", ...)
mtext(side = 1, line = 0.5, at = chrmid, text = names(chrlen), cex = 1.2)
}
if(color == "blue") {
col = rep(rgb(.122, .471, .706), length(new.qtl))
even.chr = which(seqnames(new.qtl) %in% (1:10 * 2))
col[even.chr] = rgb(.255, .624, .871)
plot(gmb, -log10(new.qtl$p.value), pch = 20, xaxt = "n",
col = col, las = 1, xlab = "", ylab = "-log10(p-value)", ...)
mtext(side = 1, line = 0.5, at = chrmid, text = names(chrlen), cex = 1.2)
}
if(color == "green") {
col = rep(rgb(.2, .627, .173), length(new.qtl))
even.chr = which(seqnames(new.qtl) %in% (1:10 * 2))
col[even.chr] = rgb(.325, .808 ,.294)
plot(gmb, -log10(new.qtl$p.value), pch = 20, xaxt = "n",
col = col, las = 1, xlab = "", ylab = "-log10(p-value)", ...)
mtext(side = 1, line = 0.5, at = chrmid, text = names(chrlen), cex = 1.2)
}
if(color == "black") {
col = rep(rgb(0,0,0), length(new.qtl))
even.chr = which(seqnames(new.qtl) %in% (1:10 * 2))
col[even.chr] = rgb(0.7,0.7,0.7)
plot(gmb, -log10(new.qtl$p.value), pch = 20, xaxt = "n",
col = col, las = 1, xlab = "", ylab = "-log10(p-value)", ...)
mtext(side = 1, line = 0.5, at = chrmid, text = names(chrlen), cex = 1.2)
}
return(new.qtl)
} # plot.hs.color.qtl
library(qqman)
library(fastmatch)
library(Kmisc)
library(lattice)
library(HZE)
HZE <- data.frame(CHR = hze@unlistData@seqnames,
BP = hze@unlistData@ranges@start,
P = hze@unlistData@elementMetadata@listData$p.value)
Gamma <- data.frame(CHR = gamma@unlistData@seqnames,
BP = gamma@unlistData@ranges@start,
P = gamma@unlistData@elementMetadata@listData$p.value)
All_Irradiated <- data.frame(CHR = allirr@unlistData@seqnames,
BP = allirr@unlistData@ranges@start,
P = allirr@unlistData@elementMetadata@listData$p.value)
Unirradiated <- data.frame(CHR = un@unlistData@seqnames,
BP = un@unlistData@ranges@start,
P = un@unlistData@elementMetadata@listData$p.value)
HZE = HZE[which(HZE$CHR == 2), ]
Gamma = Gamma[which(Gamma$CHR == 2), ]
All_Irradiated = All_Irradiated[which(All_Irradiated$CHR == 2), ]
Unirradiated = Unirradiated[which(Unirradiated$CHR == 2), ]
HZE$groups = c("HZE")
Gamma$groups = c("Gamma")
All_Irradiated$groups = c("All_Irradiated")
Unirradiated$groups = c("Unirradiated")
new = rbind(All_Irradiated, HZE, Unirradiated, Gamma)
pv = new$P
bp = new$BP
chr = as.numeric(new$CHR)
groups = new$groups
manhattan_plot(pval = pv, bp, chr, groups, cex = 2.5, xlab = "", cutoff = c(5.73, 4.48))