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.

Value

shown on or saved to the appropriate device.

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 (den Hoed et al. 2013) .

References

den Hoed M, Eijgelsheim M, Esko T, Brundel BJ, Peal DS, Evans DM, Nolte IM, Segrè AV, Holm H, Handsaker RE, Westra HJ, Johnson T, Isaacs A, Yang J, Lundby A, Zhao JH, Kim YJ, Go MJ, Almgren P, Bochud M, Boucher G, Cornelis MC, Gudbjartsson D, Hadley D, van der Harst P, Hayward C, den Heijer M, Igl W, Jackson AU, Kutalik Z, Luan J, Kemp JP, Kristiansson K, Ladenvall C, Lorentzon M, Montasser ME, Njajou OT, O'Reilly PF, Padmanabhan S, St Pourcain B, Rankinen T, Salo P, Tanaka T, Timpson NJ, Vitart V, Waite L, Wheeler W, Zhang W, Draisma HH, Feitosa MF, Kerr KF, Lind PA, Mihailov E, Onland-Moret NC, Song C, Weedon MN, Xie W, Yengo L, Absher D, Albert CM, Alonso A, Arking DE, de Bakker PI, Balkau B, Barlassina C, Benaglio P, Bis JC, Bouatia-Naji N, Brage S, Chanock SJ, Chines PS, Chung M, Darbar D, Dina C, Dörr M, Elliott P, Felix SB, Fischer K, Fuchsberger C, de Geus EJ, Goyette P, Gudnason V, Harris TB, Hartikainen AL, Havulinna AS, Heckbert SR, Hicks AA, Hofman A, Holewijn S, Hoogstra-Berends F, Hottenga JJ, Jensen MK, Johansson A, Junttila J, Kääb S, Kanon B, Ketkar S, Khaw KT, Knowles JW, Kooner AS, others (2013). “Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.” Nat Genet, 45(6), 621-31. doi:10.1038/ng.2610 .

Author

Jing Hua Zhao

Examples

if (FALSE) { # \dontrun{
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 <[email protected]>
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)
} # }