ggplot_peaks {qtl2ggplot} | R Documentation |
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
|
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
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")
[Package qtl2ggplot version 1.2.4 Index]