XY_plot: Draws an XY-plot showing allele signals and assigned dosages
In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

XY_plot

R Documentation

Draws an XY-plot showing allele signals and assigned dosages

Description

Draws an XY-plot for one markers showing the X and Y signals of each sample and their assigned dosages

Usage

XY_plot(title="", XYdat, shift=0, ploidy=NULL,
genocol="grey", pch=1, cex=1,
sel.samples=as.character(unique(XYdat$SampleName)), omit.pch=".",
omit.col=NULL, sample.groups=list(), groups.col="black", groups.pch=1,
groups.cex=1, groups.rnd=FALSE, R.thresholds=NA, R.col="black", R.lty=1)

Arguments

`title`	the main title above the plot
`XYdat`	a data frame with at least columns SampleName, X and Y; column geno (if present) is also used. Contains data for all samples, one SNP. geno is the dosage (0 .. <ploidy>), with NA or <ploidy+1> for missing dosage info
`shift`	a single integer, default 0: by how much should the geno be shifted?
`ploidy`	a single integer specifying the ploidy; default NA, only needed if there is a column geno in XYdat
`genocol`	a vector of color values to be used for plotting the sel.samples according on their geno (dosage) value; if only one value is given (default) all samples are plotted in that color
`pch`	the plot character to plot the sel.samples; default 1 is an open circle
`cex`	the relative size of the sample symbols
`sel.samples`	character vector (not a factor) with the names of the important samples: those that must be plotted in colors genocol and symbol pch
`omit.pch`	the plot character to use for the other samples, default a dot
`omit.col`	vector of two colors to use for the other samples; the first color is used for sample with a geno (dosage) value, the second color for unscored samples; recycled if needed, with NA (default) the non-selected samples are not plotted
`sample.groups`	a list specifying samples to be highlighted in a different color and/or symbol and/or size. For each group of samples the list has one vector of sample names; the list may also be empty
`groups.col`	a vector or color values, one for each item (vector of sample names) in sample.groups; recycled if shorter than sample.groups
`groups.pch`	a vector of plot symbols, one for each item in sample.groups; recycled if shorter than sample.groups
`groups.cex`	a vector of relative symbol sizes, one for each item in sample.groups; recycled if shorter than sample.groups
`groups.rnd`	FALSE (default) or TRUE. If FALSE, all samples in sample.groups are drawn in the order in which they appear in XYdat; if TRUE they are drawn in a random order. Note that the samples are never drawns in group order (except is the samples are already in group order in XYdat and groups.rnd=FALSE).
`R.thresholds`	a vector of thresholds for R to plot; is NA (default) no R thresholds are plotted
`R.col`	a vector of color values for drawing R thresholds, one for each value of R.thresholds; recycled if needed
`R.lty`	a vector of line types for drawing the R thresholds, one for each value of R.thresholds; recycled if needed