polygonChrom {ecolitk} | R Documentation |
Functions to plot circular chromosomes informations
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, ...) ecoli.len
radius |
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 |
The function chromPos2angle
is a convenience function.
The variable ecoli.len contains the size of the Escheria coli genome
considered (K12).
Except chromPos2angle
, the function are solely used for their
border effects.
laurent <laurent@cbs.dtu.dk>
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)