gap (version 1.0-23)

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.

It is possible to specify options such as xlab and ylim when the plot is requested for data in other context.

Usage

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

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()