R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Plots idiogram for one chromosome

plotIdiogram

R Documentation

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

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SNPchip)
Welcome to SNPchip version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPchip/plotIdiogram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotIdiogram
> ### Title: Plots idiogram for one chromosome
> ### Aliases: plotIdiogram plotCytoband2
> ### Keywords: aplot
> 
> ### ** Examples
> 
> plotIdiogram("1", "hg18")
NULL
> plotIdiogram("1", "hg19")
NULL
> plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE)
NULL
> ## user-defined coordinates
> plotIdiogram("1", build="hg19", cex=0.8, label.cytoband=FALSE,
+ ylim=c(0,1), cytoband.ycoords=c(0.1, 0.3))
NULL
> 
> library(oligoClasses)
Welcome to oligoClasses version 1.34.0
> 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>