plotIdiogram {SNPchip} | R Documentation |
Draw an idiogram for the specified chromosome.
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, ...)
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 |
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 |
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 |
Robert Scharpf and Jason Ting
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)