plotSnp {SNPchip} | R Documentation |
Plots copy number and genotype call versus physical position for an arbitrary number of samples and chromosomes.
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, ...)
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 |
Robert Scharpf
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))