Plot a genome scan
Plot LOD curves for a genome scan
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, ...)
x |
An object of class |
map |
A list of vectors of marker positions, as produced by
|
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. |
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.
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.
# 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.