plot_scan1: Plot a genome scan

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

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 class 'scan1'
plot(x, map, lodcolumn = 1, chr = NULL, add = FALSE, gap = NULL, ...)

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.

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. 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.

See Also

plot_coef(), plot_coefCC(), plot_snpasso()

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)

# 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)

qtl2 documentation built on May 29, 2024, 11:46 a.m.