mhtplot.trunc {gap} | R Documentation |
To generate truncated Manhattan plot, e.g., of genomewide significance (P values) or a random variable that is uniformly distributed.
mhtplot.trunc(x, chr = "CHR", bp = "BP", p = "P", snp = "SNP", col = c("gray10", "gray60"), chrlabs = NULL, suggestiveline = -log10(1e-05), genomewideline = -log10(5e-08), highlight = NULL, logp = TRUE, annotatePval = NULL, annotateTop = TRUE, cex.mtext=0.6, cex.text=0.8, mtext.line=2, cex.y= 1, y.ax.space=5, y.brk1, y.brk2, ...)
x |
A data.frame |
chr |
Chromosome |
bp |
Position |
p |
P value |
snp |
SNP |
col |
Colours |
chrlabs |
Chromosome labels |
suggestiveline |
Suggestive line |
genomewideline |
Genomewide line |
highlight |
Highlight |
logp |
log(P) |
annotatePval |
Annotate P |
annotateTop |
Annotate top |
cex.mtext |
cex.mtext |
cex.text |
cex.text |
mtext.line |
mtext.line |
cex.y |
cex.y |
y.ax.space |
y.ax.space |
y.brk1 |
y.brk1 |
y.brk2 |
y.brk2 |
... |
other options |
The plot is shown on or saved to the appropriate device.
James Peters
## Not run: # require(gap.datasets) mhtplot.trunc(mhtdata,chr = "chr", bp = "pos", p = "p", snp = "rsn", y.brk1=10, y.brk2=12) # z <- gzfile("METAL/IL.12B-1.tbl.gz") x <- read.delim(z, as.is=TRUE)[c("Chromosome","Position","P.value","MarkerName")] png("IL.12B.png", res=300, units="in", width=9, height=6) par(oma=c(0,0,0,0), mar=c(5,6.5,1,1)) mhtplot.trunc(x, chr="Chromosome", bp="Position", p="P.value", snp="MarkerName", suggestiveline=FALSE, genomewideline=-log10(5e-8), logp = TRUE, cex.mtext=2, cex.text=0.7, mtext.line=4, y.brk1=120, y.brk2=270, cex.axis=2, cex.y=2, cex=2, y.ax.space=20, col = c("blue4", "skyblue") ) dev.off() ## End(Not run)