polygonChrom: Functions to plot circular chromosomes informations

Description

Functions to plot circular chromosomes informations

Usage

cPlotCircle(radius=1, xlim=c(-2, 2), ylim=xlim, edges=300, main=NULL, main.inside, ...)
chromPos2angle(pos, len.chrom, rot=pi/2, clockwise=TRUE)
polygonChrom(begin, end, len.chrom, radius.in, radius.out, total.edges = 300, edges = max(round(abs(end - begin)/len.chrom * total.edges), 2, na.rm = TRUE), rot = pi/2, clockwise = TRUE, ...)
linesChrom(begin, end, len.chrom, radius, total.edges = 300, edges = max(round(abs(end - begin)/len.chrom * total.edges), 2, na.rm = TRUE), rot = pi/2, clockwise = TRUE, ...)
ecoli.len

Arguments

radius

xlim, ylim

range for the plot. Can be used to zoom-in a particular region.

pos

position (nucleic base coordinate)

begin

begining of the segment (nucleic base number).

end

end of the segment (nucleic base number).

len.chrom

length of the chromosome in base pairs

radius.in

inner radius

radius.out

outer radius

total.edges

total number of edges for the chromosome

edges

number of edges for the specific segment(s)

rot

rotation (default is pi / 2, bringing the angle zero at 12 o'clock)

clockwise

rotate clockwise. Default to TRUE.

main, main.inside

main titles for the plot

...

optional graphical parameters

Value

Except chromPos2angle, the function are solely used for their border effects.

Details

The function chromPos2angle is a convenience function. The variable ecoli.len contains the size of the Escheria coli genome considered (K12).

Examples

Run this code


data(ecoligenomeSYMBOL2AFFY)
data(ecoligenomeCHRLOC)

## find the operon lactose ("lac*" genes)
lac.i <- grep("^lac", ls(ecoligenomeSYMBOL2AFFY))
lac.symbol <- ls(ecoligenomeSYMBOL2AFFY)[lac.i]
lac.affy <- unlist(lapply(lac.symbol, get, envir=ecoligenomeSYMBOL2AFFY))

beg.end <- lapply(lac.affy, get, envir=ecoligenomeCHRLOC)
beg.end <- matrix(unlist(beg.end), nc=2, byrow=TRUE)

lac.o <- order(beg.end[, 1])

lac.i <- lac.i[lac.o]
lac.symbol <- lac.symbol[lac.o]
lac.affy <- lac.affy[lac.o]
beg.end <- beg.end[lac.o, ]

lac.col <- rainbow(length(lac.affy))

par(mfrow=c(2,2))

## plot

cPlotCircle(main="lac genes")
polygonChrom(beg.end[, 1], beg.end[, 2], ecoli.len, 1, 1.2, col=lac.col)
rect(0, 0, 1.1, 1.1, border="red")

cPlotCircle(xlim=c(0, 1.2), ylim=c(0, 1.1))
polygonChrom(beg.end[, 1], beg.end[, 2], ecoli.len, 1, 1.1, col=lac.col)
rect(0.4, 0.8, 0.7, 1.1, border="red")

cPlotCircle(xlim=c(.45, .5), ylim=c(.85, 1.0))
polygonChrom(beg.end[, 1], beg.end[, 2], ecoli.len, 1, 1.03, col=lac.col)

mid.genes <- apply(beg.end, 1, mean)
mid.angles <- chromPos2angle(mid.genes, ecoli.len)
xy <- polar2xy(1.03, mid.angles)
xy.labels <- data.frame(x = seq(0.45, 0.5, length=4), y = seq(0.95, 1.0, length=4))
segments(xy$x, xy$y, xy.labels$x, xy.labels$y, col=lac.col)
text(xy.labels$x, xy.labels$y, lac.symbol, col=lac.col)