plotRF {qtl} | R Documentation |
Plot recombination fractions
Description
Plot a grid showing the recombination fractions for all pairs of markers, and/or the LOD scores for tests of linkage between pairs of markers.
Usage
plotRF(x, chr, what=c("both","lod","rf"), alternate.chrid=FALSE,
zmax=12, mark.diagonal=FALSE,
col.scheme=c("viridis", "redblue"), ...)
Arguments
x |
An object of class |
chr |
Optional vector indicating the chromosomes to plot.
This should be a vector of character strings referring to chromosomes
by name; numeric values are converted to strings. Refer to
chromosomes with a preceding |
what |
Indicate whether to plot LOD scores, recombination fractions or both. |
alternate.chrid |
If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished. |
zmax |
Maximum LOD score plotted; values above this are all thresholded at this value. |
mark.diagonal |
If TRUE, include black line segments around the pixels along the diagonal, to better separate the upper left triangle from the lower right triangle. |
col.scheme |
The color palette. The default is "viridis"; see Option D at https://bids.github.io/colormap/ |
... |
Generally ignored, but you can include |
Details
Uses image
to plot a grid showing the
recombination fractions and/or LOD scores for all pairs of markers.
(The LOD scores are for a test of r = 1/2
.)
If both are plotted, the recombination fractions are in the upper left
triangle while the LOD scores are in the lower right triangle.
With col.scheme="viridis"
(the default), purple corresponds to
a large LOD score or a small recombination fraction, while yellow is
the reverse. With col.scheme="redblue"
, red corresponds to a
large LOD or a small recombination fraction, while blue is the
reverse. Note that missing values appear in light gray.
Recombination fractions are transformed by -4(\log_2{r}+1)
to make them on the same sort of scale as LOD
scores. Values of LOD or the transformed recombination fraction that
are above 12 are set to 12.
Value
None.
Author(s)
Karl W Broman, broman@wisc.edu
See Also
est.rf
, pull.rf
, plot.rfmatrix
,
image
,
badorder
, ripple
Examples
data(badorder)
badorder <- est.rf(badorder)
plotRF(badorder)
# plot just chr 1
plotRF(badorder, chr=1)
# plot just the recombination fractions
plotRF(badorder, what="rf")
# plot just the LOD scores, and just for chr 2 and 3
plotRF(badorder, chr=2:3, what="lod")