mhtplot {gap}R Documentation

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(4,6,8,10), 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.

Author(s)

Jing Hua Zhao

See Also

qqunif

Examples

## Not run: 
# 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)
par(las="2",cex=0.6)
colors <- rep(c("blue","green"),11)
mhtplot(test,colors=colors,pch=19,bg=colors)
title("A simulated example according to EPIC-Norfolk QCed SNPs")
mhtplot(test,usepos=TRUE,colors=colors,gap=10000,pch=19,bg=colors)
title("Real positions with a gap of 10000 bp between chromosomes")
#dev.off()
## End(Not run)

[Package gap version 1.0-17 Index]