gap (version 1.2.2)

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", z = NULL,
                    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

z

Z-score, i.e., BETA/SE with extremely small P

col

Colours

chrlabs

Chromosome labels

suggestiveline

Suggestive line

genomewideline

Genomewide line

highlight

Highlight

logp

log(P)

annotatePval

Annotate P

annotateTop

Annotate top

cex.mtext

axis label size

cex.text

SNP label font

mtext.line

position of the y lab

cex.y

y axis numbers

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)
# https://portals.broadinstitute.org/collaboration/
# giant/images/0/0f/Meta-analysis_Locke_et_al+UKBiobank_2018.txt.gz
gz <- gzfile("Meta-analysis_Locke_et_al+UKBiobank_2018_UPDATED.txt.gz")
BMI <- within(read.delim(gz,as.is=TRUE), {Z <- BETA/SE})
library(Rmpfr)
within(subset(BMI, P==0), {P <- format(2*pnorm(mpfr(abs(BETA/SE),100),lower.tail=FALSE))})
png("BMI.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(BMI, chr="CHR", bp="POS", p="P", snp="SNP", z = "Z",
              suggestiveline=FALSE, genomewideline=-log10(1e-8), logp = TRUE,
              cex.mtext=0.6, cex.text=0.7,
              mtext.line=4, y.brk1=200, y.brk2=280, cex.axis=0.6, cex.y=0.6, cex=0.5,
              y.ax.space=20,
              col = c("blue4", "skyblue")
)
dev.off()
# }