gap (version 1.6)

circos.mhtplot2: Another circos Manhattan plot

Description

Another circos Manhattan plot

Usage

circos.mhtplot2(dat, labs, species = "hg18", ticks = 0:3 * 10, ymax = 30)

Value

There is no return value but a plot.

Arguments

dat

Data to be plotted with variables chr, pos, log10p.

labs

Data on labels.

species

Genome build.

ticks

Tick positions.

ymax

maximum value for y-axis.

Details

This is adapted from work for a recent publication. It enables a y-axis to the -log10(P) for association statistics

Examples

if (FALSE) {
require(gap.datasets)
library(dplyr)
glist <- c("IRS1","SPRY2","FTO","GRIK3","SNED1","HTR1A","MARCH3","WISP3",
           "PPP1R3B","RP1L1","FDFT1","SLC39A14","GFRA1","MC4R")
testdat <- mhtdata[c("chr","pos","p","gene","start","end")] %>%
           rename(log10p=p) %>%
           mutate(chr=paste0("chr",chr),log10p=-log10(log10p))
dat <- mutate(testdat,start=pos,end=pos) %>%
       select(chr,start,end,log10p)
labs <- subset(testdat,gene %in% glist) %>%
        group_by(gene,chr,start,end) %>%
        summarize() %>%
        mutate(cols="blue") %>%
        select(chr,start,end,gene,cols)
labs[2,"cols"] <- "red"
ticks <- 0:3*5
circos.mhtplot2(dat,labs,ticks=ticks,ymax=max(ticks))
# https://www.rapidtables.com/web/color/RGB_Color.html
}