plotpeaks: Plot position of trait vs. position of QTL

In atbroman/neqtl: Tools for analyzing expression QTL by position on genome

Description

Plots trait position, based on annotation against position of QTL, based on position of maximum LOD score. Uses output from peaks function, CIS traits are shown in grayscale.

Usage

plotpeaks(pos.peaks,
map=NULL, 
n.col = 256,
cbreaks = quantile(pos.peaks$peaks.lod,
          probs = seq(0, 1, length = n.col+ 1)),
chr.peaks = levels(factor(pos.peaks$peaks.chr,exclude=NULL)),
chr.trait = levels(factor(pos.peaks$trait.chr,exclude=NULL)),
clab.peaks = chr.peaks,
clab.trait = chr.trait,
xlab = "Chromosome of Peak Score",
ylab = "Chromosome of Transcript",
col.legend = TRUE,
llims = c(-0.08, 0.3, -0.12, -0.14),
lticks = c(0.025, 0.25, 0.5, 0.75, 0.975),
lcex = 0.8,
 ...)

Arguments

pos.peaks	peaks element from peaks function. peaks is a data.frame. See Details
map	map object from cross object, used to determine chromosome lengths; if not available, estimated from pos.peaks
n.col	Number of colors to use, default is 256
cbreaks	Breaks to categorize LOD score, length(cbreaks) = n.col+1, see Details
chr.peaks	Character vector of subset of peak chromosomes, defaults to all chromosomes
chr.trait	Character vector of trait chromosomes, defaults to all chromosomes
clab.peaks	Character vector for x-axis labels, must be a subset of chr.peaks
clab.trait	Character vector for y-axis labels, must be a subset of chr.trait
xlab	x-axis label
ylab	y-axis label
col.legend	logical, TRUE to add a color legend along the x-axis; colors correspond to LOD scores
llims	numeric vector of the form c(x0,xl,y0,y1) as a fraction of the plotting area, where legend should be placed
lticks	numeric vector between 0 and 1 indicating quantiles of LOD categories to label in the legend
lcex	magnification of legend text size relative to the currrent setting of cex
...	additional paramters for points and text

Details

For plotting purposes, the pos.peaks should have non-missing trait.pos for all traits; occasionally, traits will reside on chromosomes that are not part of the marker set, and will have unknown cM positions. In this case, Mb positions may be substituted to show trans relationships.

The default color categories are divided by equally spaced quantiles of the peak LOD scores for maximum color range.

Value

Outputs a plot

Author(s)

Brian Yandell and Aimee Teo Broman

See Also

peaks cistrans (from qtlview library)

Examples

data(fake.f2expr)
fake.f2expr <- calc.genoprob(fake.f2expr)

scan.f2 <- scanone(fake.f2expr,pheno.col=1:100, method="hk")
maxlod.f2 <- maxlod(scan.f2)
sigpos.f2 <- maxlod.sigpos(maxlod.f2,sig.lod=3)

## Fake annotation ##
data(fake.annot)

peaks.f2 <- peaks(maxlod.f2,sigpos.f2,fake.annot)

plotpeaks(peaks.f2$peaks,map=pull.map(fake.f2expr))

atbroman/neqtl documentation built on May 10, 2019, 2:08 p.m.