plotSnp {SNPchip}R Documentation

Plots copy number and genotype calls.

Description

Plots copy number and genotype call versus physical position for an arbitrary number of samples and chromosomes.

Usage

plotSnp(object, chromosomes, samples, snpId = c(NA, 1e+06), oma = c(5, 4, 4, 0.5), mar = c(0.5, 0, 0.5, 0.2), width.right = NULL, showLayout = FALSE, plot = TRUE, col = c("royalblue", "red", "royalblue", "green3"), bg = rep("white", 4), cex = c(2, 3, 2, 2), pch = rep(".", 4), col.centromere = c("bisque", NA), bw = FALSE, lwd = 2, col.axis = "brown", cex.axis = 1, cex.main = 1, cex.lab = 1, xlim = NULL, ylim = NULL, log = "", xaxis.side = rep(c(1, 3), length.out = length(chromosomes)), xaxs = "i", xaxt = "n", yaxs = "i", yaxt = "n", xlab = "", ylab = "", lab = c(2, 5, 7), adj = 0, main = "", legend = c(TRUE, TRUE), legend.panel = c(TRUE, FALSE), legend.location = c("topright", "bottomright"), legend.bty = c("n", "n"), legend.col = c("white", "white"), ncol = 2, cex.legend = c(1, 1), digits = 3, pt.cex = cex.legend * 1.5, bty = "n", addCytoband = FALSE, height.cytoband = 0.5, ...)

Arguments

object Object of class AnnotatedSnpCopyNumberSet or AnnotatedSnpSet
chromosomes Vector of character strings for chromosome number. Chromosomes will be plotted in the order given.
samples Vector of integers indicating sample number.
snpId Not yet implemented.
oma See par
mar See par
width.right Width of panel for the legend relative to the width of the smallest chromosome.
showLayout Logical for whether to display the output of layout for plotting
plot Logical. If FALSE, only the output from layout is displayed.
col A character or numerical vector indicating the color to plot genotype call: AA color, AB color, BB color, no call color. For AnnotatedSnpCopyNumberSet, only the first color is used.
bg A character or numerical vector indicating the background color for the plotting symbols. Possible to specify a different background for each genotype call in the same order as col.
cex A numerical vector of plotting symbol size in the same order as col.
pch A character or numerical vector of plotting symbol size in the same order as col.
col.centromere Vector of length two: color of centromere and color for the centromere border.
bw Converts all colors to grayscale.
lwd See par
col.axis See par
cex.axis See par
cex.main See par
cex.lab See par
xlim See par
ylim See par
log See par
xaxis.side Vector of integers indicating whether to plot the x-axis on the top (3) or bottom (1) for each sample. The default is to alternate top/bottom.
xaxs See par
xaxt See par
yaxs See par
yaxt See par
xlab See par
ylab See par
lab See par
adj See par
main See par
legend Logical vector of length 2. If both are TRUE, a legend for descriptive statistics (legend 1) and plotting symbols (legend 2) are generated.
legend.panel Logical vector of length 2. Whether to draw the legends on a separate panel.
legend.location Character vector of length 2. Where to draw the legends. See legend.
legend.bty Character vector of length 2. See the argument bty in function legend.
legend.col Character vector of length 2. See the argument bty in function legend.
ncol Number of columns in legend for plotting symbols. See legend.
cex.legend Same as argument cex in function legend.
digits Rounds values in legend to the number of digits specified.
pt.cex See legend
bty See par
addCytoband Logical indicating whether to add a cytoband.
height.cytoband Height of cytoband relative to height of samples.
... Additional arguments

Details

Value

Note

Author(s)

Robert Scharpf

References

See Also

par, plot, legend

Examples

data(annSnpset)
plotSnp(annSnpset, chromosomes=c(1:22, "X"), 
        samples=1:4, width.right=10, cex.axis=1, lab=c(3, 3, 5),
        cex.lab=1.2, cex.legend=c(1, 1.2))

[Package SNPchip version 1.0.0 Index]