SNPchip (version 2.18.0)

plotIdiogram: Plots idiogram for one chromosome

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

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)