rc.initialize: Initialize Circos Plot Parameters
In NetWeaver: Graphic Presentation of Complex Genomic and Network Data Analysis

Description Usage Arguments Details Author(s) See Also Examples

Setup default parameter for Circos plot.

1 2	rc.initialize(cyto.info, num.tracks=NULL, chr.order=NULL, stepUnit=10^7, Layout=c('circular','landscape'), params=list())

`cyto.info`	data.frame, see `Details`.
`num.tracks`	integer, number of tracks.
`chr.order`	character vector of chromosome ids specifying the ordering of chromosomes.
`stepUnit`	integer, smoothing factor for faster plotting.
`Layout`	layout for plotting.
`params`	a list of named items. See `Details`.

cyto.info is a data.frame of chromosomal position ordered cytobands, with columns: Chr, Start, End, Stain, and any additional information (like band color), where Chr is chromosome name, Start and End are the start and end positions on the chromosome, and Stain is the cyto stain. The stain is normally one of the "gneg", "acen", "stalk", "gvar", "gpos", "gpos100", "gpos75", "gpos66", "gpos50", "gpos33", and "gpos25", which will be plotted by color "white", "red", "steelblue", "lightgrey", "black", "black", "gray40", "gray50", "gray60", "gray70" and "gray80", accordingly. Customized colors for the cyto bands can be specified in an additional column named "BandColor".

Additional plot parameters can be specified through argument params, including:

color.line, color for lines and links, default "black".
chr.padding, padding between chromsomes is a fraction of the total chromosome sizes, default 0.1.
track.padding, paddings between tracks is a fraction of the track height, default 0.1
track.height, track height, default 0.15.
radius radius of the circos, default 1.
sector.degree, a value between 0 and 2*Pi (the default) specifying the circular sector size of the circos plot.

After initialization, the parameter settings can be retrieved by rc.get.params.

Noted that while cyto.info requires input to be in a form of chromosome cytobands, the input is not limited to genomic features. As illustrated in example data Modules, complex features of gene coexpression network modules can also be plotted with the current circos visualization technique.

Minghui Wang <m.h.wang@live.com>

rc.get.params, rc.reset.params, rc.plot.ideogram, rc.plot.histogram, rc.plot.mHistogram, rc.plot.barchart, rc.plot.link, rc.plot.ribbon, Modules

library(NetWeaver)
options(stringsAsFactors=FALSE)
## set fake Cyto data
Cyto=data.frame(Chr=paste0('C',1:20), Start=1, End=100, BandColor=colors()[2:21])

## initialize circos
#firstly set number of tracks, should be larger than the actual number of tracks
#used for plotting in order to leave sufficient sapce in the middle
num.tracks=9 
rc.initialize(Cyto, num.tracks=num.tracks, params=list(chr.padding=0.1,sector.degree=2*pi))

##retrieve parameters
params=rc.get.params()
#make plot area
rc.plot.area(size=0.95)

##plot ideogram on track 1 and 2 (start from the outside to inside)
track.num=1:2
rc.plot.ideogram(track.num, plot.band=TRUE, plot.chromosome.id=TRUE)

##plot histogram/barchart that span multiple chromosomes
MultHistData=data.frame(Chr1=paste0('C',seq(1,18,3)), Start1=50, 
	Chr2=paste0('C',seq(3,20,3)), End2=20, Col=1:6)
track.num=3
rc.plot.mHistogram(MultHistData, track.id=track.num, data.col=5,
	color.col=5, fixed.height=FALSE)

##plot histogram that occupies two tracks 4 and 5
HistData=data.frame(Chr=paste0('C',1:20), Start=1, End=50, Data=runif(20))
params$color.hist <- 'black'
rc.reset.params(params)
track.num=5
rc.plot.histogram(HistData, track.num, data.col=4, fixed.height=FALSE, 
	track.border=NA, custom.track.height=params$track.height*2)

##plot heatmap on track 6
HeatData=data.frame(Chr=paste0('C',1:20), Start=1,End=100, Data=1:20)
colfuncHeat=function(n) rev(heat.colors(n))
track.num=track.num+1
rc.plot.histogram(HeatData, track.num, data.col=4, color.gradient=colfuncHeat(50),
	fixed.height=TRUE)

##plot stacked barchart on track 7
BarData=data.frame(Chr=paste0('C',1:20), Start=1, 
	End=seq(10,86,length.out=20), Data=matrix(runif(20*4),nrow=20))
track.num=track.num+1
rc.plot.barchart(BarData, track.num, data.col=4:7)

##plot links in the middle
LinkData=data.frame(Chr1=sample(Cyto$Chr,40,replace=TRUE), Pos1=20, 
	Chr2=sample(Cyto$Chr,40,replace=TRUE),Pos2=20, Data=runif(20))
LinkData=LinkData[LinkData$Chr1 != LinkData$Chr2,]
params$color.line='blue'
rc.reset.params(params)
track.num=track.num+1
rc.plot.link(LinkData, track.num, data.col=4, arrow.length=0.1)
ribbonData=data.frame(Chr1=c('C1','C3'), Start1=c(10,10), End1=c(40,40),
	Chr2=c('C17','C10'), Start2=20, End2=60, Col=c('red','brown'))
rc.plot.ribbon(ribbonData, track.num, color.col='Col', twist=TRUE)
#label track id
rc.plot.track.id(2:7, col=2)
#add text label
rc.plot.text(data.frame(Chr='C3',Pos=50,Label='GeneX'), 
	track.id=3,srt=45,cex=0.8,col='blue')
#add line mark
rc.plot.line(data.frame(Chr='C19',Pos=seq(10,90,by=15),Col='red'), 
	track.id=3, color.col=3,arrow.length=0.2)