plot_peaks: Plot QTL peak locations

In rqtl/qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Plot QTL peak locations

Description

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

Usage

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

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. The default is 1% of the total genome length.
lod_labels	If TRUE, plot LOD scores near the intervals. Uses three hidden graphics parameters, label_gap (distance between CI and LOD text label), label_left (vector that indicates whether the labels should go on the left side; TRUE=on left, FALSE=on right, NA=put into larger gap on that chromosome), and label_cex that controls the size of these labels
...	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

find_peaks(), plot_lodpeaks()

Examples

# 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))

rqtl/qtl2 documentation built on March 20, 2024, 6:35 p.m.