ggplot_peaks: Plot QTL peak locations

In qtl2ggplot: Data Visualization for QTL Experiments

Plot QTL peak locations

Description

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

Usage

ggplot_peaks(
  peaks,
  map,
  chr = NULL,
  tick_height = 0.3,
  gap = 25,
  bgcolor = "gray90",
  altbgcolor = "gray85",
  ...
)

Arguments

peaks	Data frame such as that produced by 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.
bgcolor	Background color for the plot.
altbgcolor	Background color for alternate chromosomes.
...	Additional graphics parameters

Value

None.

See Also

find_peaks

Examples

# load qtl2 package for data and genoprob calculation
library(qtl2)

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

# 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
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)

# color peaks above 6 red; only show chromosomes with peaks
plot_peaks(peaks, map)
peaks$col <- (peaks$lod > 6)

ggplot_peaks(peaks, map[names(map) %in% peaks$chr], col = c("blue","red"),
           legend.title = "LOD > 6")

qtl2ggplot documentation built on Aug. 8, 2025, 6:06 p.m.