gap (version 1.0-22)

mhtplot: Manhattan plot of p values

Description

To generate Manhattan plot of genomewide significance (p values). It could also be used for any random variable that is uniformly distributed. By default, a log10-transformation is applied so that a different set of cutoffs can be more appropriate. Note that with real chromosomal positions, it is also appropriate to plot and some but not all chromosomes.

Usage

mhtplot(data, usepos=FALSE, logscale=TRUE, base=10, cutoffs=c(4,6,8), colors=NULL, labels=NULL, xlab=NULL, gap=NULL, ...)

Arguments

data

a data frame with three columns representing chromosome, position and p values

usepos

a flag to use real chromosomal positions as composed to ordinal positions

logscale

a flag to indicate if p value is to be log-transformed

base

the base of the logarithm

cutoffs

the cut-offs where horizontal line(s) are drawn

colors

the color for different chromosome(s), and random if unspecified

labels

labels for the x-axis

xlab

an enforcement of the x-axis when the plot is requested for data in other context

gap

gap between chromosomes

...

other options in compatible with the R plot function

Value

• The plot is shown on or saved to the appropriate device.

See Also

qqunif

Examples

# foo example
test <- matrix(c(1,1,4,1,1,6,1,10,3,2,1,5,2,2,6,2,4,8),byrow=TRUE,6)
mhtplot(test)
mhtplot(test,logscale=F)

# fake example with Affy500k data
affy <-c(40220, 41400, 33801, 32334, 32056, 31470, 25835, 27457, 22864, 28501, 26273, 
         24954, 19188, 15721, 14356, 15309, 11281, 14881, 6399, 12400, 7125, 6207)
CM <- cumsum(affy)
n.markers <- sum(affy)
n.chr <- length(affy)
test <- data.frame(chr=rep(1:n.chr,affy),pos=1:n.markers,p=runif(n.markers))

# to reduce size of the plot
# bitmap("mhtplot.bmp",res=72*5)
oldpar <- par()
par(las="2",cex=0.6)
colors <- rep(c("blue","green"),11)
# other colors, e.g.
# colors <- c("red","blue","green","cyan","yellow","gray","magenta","red","blue","green",
#             "cyan","yellow","gray","magenta","red","blue","green","cyan","yellow","gray","magenta","red")
mhtplot(test,colors=colors,pch=19,bg=colors)
title("A simulated example according to EPIC-Norfolk QCed SNPs")
par(cex.axis=1.3)
mhtplot(test,usepos=TRUE,colors=colors,gap=10000,pch=19,bg=colors)
title("Real positions with a gap of 10000 bp between chromosomes")
box()
par(oldpar)
# dev.off()