Description Usage Arguments Value Hidden graphics parameters See Also Examples
Plot LOD curves for a genome scan
1 2 3 4 5 6 |
x |
Output of |
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. |
... |
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.
plot_coef()
, plot_coefCC()
, plot_snpasso()
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | # load qtl2geno package for data and genoprob calculation
library(qtl2geno)
# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
# 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
library(qtl2scan)
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)
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