| plot.errorlod {qtl} | R Documentation |
Plot a grid of the LOD scores indicating which genotypes are likely to be in error.
## S3 method for class 'errorlod':
plot(x, chr, ind, breaks=c(-Inf,2,3,4.5,Inf),
col=c("white","gray85","hotpink","purple3"),
alternate.chrid=FALSE, ...)
x |
An object of class cross. See
read.cross for details. |
chr |
Optional vector indicating the chromosomes to be drawn in
the 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 - to have all chromosomes but
those considered. A logical (TRUE/FALSE) vector may also be used. |
ind |
Indicates the individuals for which the error LOD scores
should be plotted (passed to subset.cross). |
breaks |
A set of breakpoints for the colors; must give one more breakpoint than color. Intervals are open on the left and closed on the right, except for the lowest interval. |
col |
A vector of colors to appear in the image. |
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. |
... |
Ignored at this point. |
Uses image to plot a grid with different shades
of pixels to indicate which genotypes are likely to be in error.
Darker pixels have higher error LOD scores: LOD <= 2 in white; 2 < LOD <= 3 in gray; 3 < LOD <= 4.5 in pink; LOD > 4.5 in purple.
None.
Karl W Broman, kbroman@biostat.wisc.edu
Lincoln, S. E. and Lander, E. S. (1992) Systematic detection of errors in genetic linkage data. Genomics 14, 604–610.
calc.errorlod,
top.errorlod, image,
subset.cross, plot.geno
data(hyper) # Calculate error LOD scores hyper <- calc.errorlod(hyper,error.prob=0.01) # plot the error LOD scores; print those above a specified cutoff plot.errorlod(hyper) plot.errorlod(hyper,chr=1)