mhtplot2: Manhattan plot with annotations

In gap: Genetic Analysis Package

Manhattan plot with annotations

Description

Manhattan plot with annotations

Usage

mhtplot2(data, control = mht.control(), hcontrol = hmht.control(), ...)

Arguments

data	a data frame with three columns representing chromosome, position and p values.
control	A list produced by mht.control() controlling plot behaviour.
hcontrol	A list produced by hmht.control() defining highlighted markers or regions and labels.
...	Additional graphical arguments passed to graphics::plot() (e.g. pch, bg, xlab, ylab, ylim). If mar is supplied, the default margins are not modified.

Details

To generate Manhattan plot with annotations. The function is generic and for instance could be used for genomewide p values or any random variable that is uniformly distributed. By default, a log10-transformation is applied. Note that with real chromosomal positions, it is also appropriate to plot and some but not all chromosomes.

It is possible to specify options such as xlab, ylim and font family when the plot is requested for data in other context. The example uses only chromosomes 14 and 20 of \insertCitedenhoed13gap.

Value

shown on or saved to the appropriate device.

Author(s)

Jing Hua Zhao

References

\insertRef

denhoed13gap

Examples

## Not run: 
mdata <- within(hr1420,{
  c1<-colour==1
  c2<-colour==2
  c3<-colour==3
  colour[c1] <- 62
  colour[c2] <- 73
  colour[c3] <- 552
})
mdata <- mdata[,c("CHR","POS","P","gene","colour")]
ops <- mht.control(colors=rep(c("lightgray","gray"),11),yline=1.5,xline=2)
hops <- hmht.control(data=subset(mdata,!is.na(gene)),boxed=TRUE)
v <- "Verdana"
ifelse(Sys.info()['sysname']=="Windows", windowsFonts(ffamily=windowsFont(v)),
       ffamily <- v)
tiff("mh.tiff", width=.03937*189, height=.03937*189/2, units="in", res=1200,
     compress="lzw")
par(las=2, xpd=TRUE, cex.axis=1.8, cex=0.4)
mhtplot2(with(mdata,cbind(CHR,POS,P,colour)),ops,hops,pch=19,
         ylab=expression(paste(plain("-"),log[10],plain("p-value"),sep=" ")),
         family="ffamily")
axis(2,pos=2,at=seq(0,25,5),family="ffamily",cex=0.5,cex.axis=1.1)
dev.off()

# To exemplify the use of chr, pos and p without gene annotation
# in response to query from Vallejo, Roger <[e-mail]>
opar <- par()
par(cex=0.4)
ops <- mht.control(colors=rep(c("lightgray","lightblue"),11),yline=2.5,xline=2)
mhtplot2(data.frame(mhtdata[,c("chr","pos","p")],gene=NA,color=NA),ops,xlab="",ylab="")
axis(2,at=1:16)
title("data in mhtplot used by mhtplot2")
par(opar)

## End(Not run)

gap documentation built on May 28, 2026, 9:07 a.m.