Mirror Manhattan Plot
3
1
Entering edit mode
4.7 years ago
jennysjaarda ▴ 10

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

qqman manhattan GWAS plot R • 3.6k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

They are called Miami plot. (Because of the reflection of buildings on Miami biscayne bay)

Related SO post:

ADD REPLY
2
Entering edit mode
23 months ago
bernatgel ★ 3.1k

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")

Mirrored manhattan plot

ADD COMMENT
1
Entering edit mode
8 months ago
DM ▴ 30

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()

GWAS Miami plot

ADD COMMENT
1
Entering edit mode
12 weeks ago
Jimbou ▴ 830

You can try a ggplot-tidyverse solution based on ggfastman.

library(tidyverse)
library(ggfastman)
data("gwas_data")
gwas_data %>% 
  mutate( gr= "Study 1") %>% 
  mutate(pvalue=log10(pvalue)) %>% 
  # rbind a second study with pvalues with other sign.
  bind_rows(., mutate(., gr= "Study 2",
                      pvalue = -pvalue)) %>% 
  # plot the points 
  fast_manhattan(., build = "hg18", speed = "fast",log10p = F, dodge_x = T,pointsize = 2.1, pixels = c(1000,500)) + 
  # add significance line
  geom_hline(data= . %>% group_by(gr) %>% slice(1), aes(yintercept = ifelse(pvalue>0, -log10(5e-08),log10(5e-08))),color ="deeppink") + 
  coord_flip()+
  scale_y_continuous(expression(-log[10](italic(p))),breaks= seq(-90,80,10), labels = abs(seq(-90,80,10)), expand = c(0.01, 0))+
  facet_wrap(~gr, scales = "free_x")+ 
  ggplot2::guides(y = guide_axis(n.dodge = 2), x = guide_axis())+
  theme_bw()

enter image description here

ADD COMMENT

Login before adding your answer.

Traffic: 2338 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6