plot_peaks: Plot QTL peak locations

In rqtl/qtl2plot: Data Visualization for QTL Experiments

Description

Plot QTL peak locations (possibly with intervals) for multiple traits.

Usage

plot_peaks(peaks, map, chr = NULL, tick_height = 0.3, gap = 25, ...)

Arguments

peaks	Data frame such as that produced by qtl2scan::find_peaks()) containing columns chr, pos, lodindex, and lodcolumn. May also contain columns ci_lo and ci_hi, in which case intervals will be plotted.
map	Marker map, used to get chromosome lengths (and start and end positions).
chr	Selected chromosomes to plot; a vector of character strings.
tick_height	Height of tick marks at the peaks (a number between 0 and 1).
gap	Gap between chromosomes.
...	Additional graphics parameters

Value

None.

Hidden graphics parameters

A number of graphics parameters can be passed via .... For example, bgcolor to control the background color and altbgcolor to control the background color on alternate chromosomes. These are not included as formal parameters in order to avoid cluttering the function definition.

See Also

qtl2scan::find_peaks()

Examples

# load qtl2geno package for data and genoprob calculation
library(qtl2geno)

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))

# insert pseudomarkers into map
map <- insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- calc_genoprob(iron, map, error_prob=0.002)

# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- get_x_covar(iron)

# perform genome scan
library(qtl2scan)
out <- scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)

# find peaks above lod=3.5 (and calculate 1.5-LOD support intervals)
peaks <- find_peaks(out, map, threshold=3.5, drop=1.5)

plot_peaks(peaks, map)

rqtl/qtl2plot documentation built on May 28, 2019, 2:36 a.m.