Plot QTL peak locations
Plot QTL peak locations (possibly with intervals) for multiple traits.
plot_peaks( peaks, map, chr = NULL, tick_height = 0.3, gap = NULL, lod_labels = FALSE, ... )
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. The default is 1% of the total genome length. |
lod_labels |
If TRUE, plot LOD scores near the intervals. Uses
three hidden graphics parameters, |
... |
Additional graphics parameters |
None.
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.
# 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)
plot_peaks(peaks, map)
# show LOD scores
plot_peaks(peaks, map, lod_labels=TRUE)
# show LOD scores, controlling whether they go on the left or right
plot_peaks(peaks, map, lod_labels=TRUE,
label_left=c(TRUE, TRUE, TRUE, FALSE, TRUE, FALSE))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.