plot_scan1: Plot a genome scan

Description

Plot LOD curves for a genome scan

Usage

plot_scan1(x, map, lodcolumn = 1, chr = NULL, add = FALSE, gap = NULL, ...)
# S3 method for scan1
plot(x, map, lodcolumn = 1, chr = NULL, add = FALSE, gap = NULL, ...)

Value

None.

Arguments

x: An object of class "scan1", as output by scan1().
map: A list of vectors of marker positions, as produced by insert_pseudomarkers().
lodcolumn: LOD score column to plot (a numeric index, or a character string for a column name). Only one value allowed.
chr: Selected chromosomes to plot; a vector of character strings.
add: If TRUE, add to current plot (must have same map and chromosomes).
gap: Gap between chromosomes. The default is 1% of the total genome length.
...: Additional graphics parameters.

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. col controls the color of lines/curves; altcol can be used if you want alternative chromosomes in different colors. These are not included as formal parameters in order to avoid cluttering the function definition.

Examples

Run this code

# 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)

# plot the results for selected chromosomes
ylim <- c(0, maxlod(out)*1.02) # need to strip class to get overall max LOD
chr <- c(2,7,8,9,15,16)
plot(out, map, chr=chr, ylim=ylim)
plot(out, map, lodcolumn=2, chr=chr, col="violetred", add=TRUE)
legend("topleft", lwd=2, col=c("darkslateblue", "violetred"), colnames(out),
       bg="gray90")

# plot just one chromosome
plot(out, map, chr=8, ylim=ylim)
plot(out, map, chr=8, lodcolumn=2, col="violetred", add=TRUE)

# lodcolumn can also be a column name
plot(out, map, lodcolumn="liver", ylim=ylim)
plot(out, map, lodcolumn="spleen", col="violetred", add=TRUE)