mhtplot {gap} | R Documentation |
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.
mhtplot(data, usepos=FALSE, logscale=TRUE, base=10, cutoffs=c(4,6,8), colors=NULL, labels=NULL, xlab=NULL, gap=NULL, ...)
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 |
The plot is shown on or saved to the appropriate device.
Jing Hua Zhao
## Not run: # 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() ## End(Not run)