Mirror Manhattan Plot

Question

[jennysjaarda]

Does anyone know how to adapt the qqman Manhattan plot (or other function) to create a mirror image Manhattan plot as seen here (i.e. reverse the axis on the bottom plot): https://www.researchgate.net/figure/284888365_fig2_Fig-2-Manhattan-plot-of-the-Burmese-head-deformity-GWAS-and-SNPs-genotypes-within

[Maxime Lamontagne]

Did you try to invert the ylim option. Intead of c(0,10) for example, try c(10,0).

Answer 1

[bernatgel]

To plot mirrored manhattan plots you can use kpPlotManhattan from the karyoploteR Bioconductor package.

kp <- plotKaryotype(plot.type=4)
kpAddLabels(kp, labels = "Trait 1", srt=90, pos=3, r0=0.5, r1=1, cex=1.8, label.margin = 0.025)
kpAxis(kp, ymin=0, ymax=10, r0=0.5)
kp <- kpPlotManhattan(kp, data=ds$snps, highlight = ds$peaks, r0=0.5, r1=1, ymax=10)
kpAddLabels(kp, labels = "Trait 2", srt=90, pos=3, r0=0, r1=0.5, cex=1.8, label.margin = 0.025)
kpAxis(kp, ymin=0, ymax=10, r0=0.5, r1=0, tick.pos = c(5,10))
kp <- kpPlotManhattan(kp, data=createDataset()$snps, r0=0.5, r1=0, ymax=10, points.col = "2blues")

Answer 2

[DM]

Hi,

You could do something similar to this

library(qqman)
par(mfrow=c(2,1))
par(mar=c(0,5,3,3))
manhattan(gwasResults,ylim=c(0,10),cex=2.2,cex.lab=2.5,font.lab=2,font.axis=2,cex.axis=1.6,las=2,font=4)
par(mar=c(5,5,3,3))
manhattan(gwasResults,ylim=c(10,0),cex=2.2,cex.lab=2.5,font.lab=2,font.axis=2,cex.axis=1.6,las=2,font=4,xlab="",xaxt="n")
dev.off()