gap (version 1.2.1)

mhtplot.trunc: Truncated Manhattan plot

Description

To generate truncated Manhattan plot, e.g., of genomewide significance (P values) or a random variable that is uniformly distributed.

Usage

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, ...)

Arguments

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

Value

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

See Also

mhtplot

Examples

# 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()
# }