plotIdiogram: Plots idiogram for one chromosome

In SNPchip: Visualizations for copy number alterations

Description

Draw an idiogram for the specified chromosome.

Usage

plotIdiogram(chromosome, build, cytoband, cytoband.ycoords, xlim, ylim=c(0, 2),
new=TRUE, label.cytoband=TRUE, label.y=NULL, srt, cex.axis=1,
outer=FALSE, taper=0.15, verbose=FALSE, unit=c("bp", "Mb"),
is.lattice=FALSE,...)
plotCytoband2(chromosome, build, cytoband, xlim, xaxs="r", new=TRUE,
label.cytoband=TRUE, cex.axis=1, outer=FALSE, verbose=TRUE, ...)

Arguments

chromosome	character string or integer: which chromosome to draw the cytoband
build	UCSC genome build. Supported builds are "hg18" and "hg19".
cytoband	data.frame containing cytoband information
cytoband.ycoords	numeric: y coordinates
xlim	x-axis limits
xaxs	numeric. See par
ylim	y-axis limits
new	logical: new plotting device
label.cytoband	logical: if TRUE, labels the cytobands
label.y	numeric: height (y-coordinate) for cytoband label
srt	string rotation for cytoband labels. See par
cex.axis	size of cytoband labels. See par
outer	logical: whether to draw the labels in the outer margins. See par
taper	tapering for the ends of the cytoband
verbose	Logical. If TRUE, displays human genome build used to annotated the cytoband coordinates.
unit	Character string indicating the unit for physical position on the x-axis. Available options are basepairs (bp) or Mb.
is.lattice	logical indicating whether your drawing the cytoband on a lattice graphic.
...	additional arguments to plot

Author(s)

Robert Scharpf and Jason Ting

Examples

plotIdiogram("1", "hg18")
plotIdiogram("1", "hg19")
plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE)
## user-defined coordinates
plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE,
ylim=c(0,1), cytoband.ycoords=c(0.1, 0.3))

library(oligoClasses)
sl <- getSequenceLengths("hg19")[c(paste("chr", 1:22, sep=""), "chrX", "chrY")]
ybottom <- seq(0, 1, length.out=length(sl)) - 0.01
ytop <- seq(0, 1, length.out=length(sl)) + 0.01
for(i in seq_along(sl)){
	chr <- names(sl)[i]
	if(i == 1){
		plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE, ylim=c(-0.05,1.05), cytoband.ycoords=c(ybottom[1], ytop[1]),
			     xlim=c(0, max(sl)))
	}
	if(i > 1){
		plotIdiogram(names(sl)[i], build="hg19", cex=0.8, label.cytoband=FALSE, cytoband.ycoords=c(ybottom[i], ytop[i]), new=FALSE)
	}
}
axis(1, at=pretty(c(0, max(sl)), n=10), labels=pretty(c(0, max(sl)), n=10)/1e6, cex.axis=0.8)
mtext("position (Mb)", 1, line=2)
par(las=1)
axis(2, at=ybottom+0.01, names(sl), cex.axis=0.6)

SNPchip documentation built on Oct. 31, 2019, 2:07 a.m.