Get x-axis locations in scanone plot
Get x-axis locations for given cM positions on given chromosomes in a
plot from plot.scanone)
xaxisloc.scanone(out, thechr, thepos, chr, gap=25)
out |
An object of class |
thechr |
Chromosome IDs at which x-axis locations are to be determined. |
thepos |
Chromosome positions at which x-axis locations are to be determined. |
chr |
Optional vector specifying which chromosomes were plotted.
This must be identical to what was used in the call to
|
gap |
Gap separating chromosomes (in cM). This must be identical
to what was used in the call to |
This function allows you to identify the x-axis locations in a plot of
genome scan results, produced by
plot.scanone. This is useful for adding
annotations, such as text or arrows.
The arguments out, chr, and gap must match what
was used in the call to plot.scanone.
The arguments thechr and thepos indicate the genomic
positions for which x-axis locations are desired. If they both have
length > 1, they must have the same length. If one has length > 1 and
one has length 1, the one with length 1 is expanded to match.
A numeric vector of x-axis locations.
Karl W Broman, broman@wisc.edu
data(hyper) hyper <- calc.genoprob(hyper) out <- scanone(hyper, method="hk") plot(out, chr=c(1, 4, 6, 15)) # add arrow and text to indicate peak LOD score mxout <- max(out) x <- xaxisloc.scanone(out, mxout$chr, mxout$pos, chr=c(1,4,6,15)) arrows(x+30, mxout$lod, x+5, mxout$lod, len=0.1, col="blue") text(x+35, mxout$lod, "the peak", col="blue", adj=c(0, 0.5))
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