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Last data update: 2014.03.03

R: Functions to plot circular chromosomes informations

polygonChrom

R Documentation

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`	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

Details

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

Value

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

Author(s)

laurent <laurent@cbs.dtu.dk>

Examples


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)

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(ecolitk)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ecolitk/polygonChrom.Rd_%03d_medium.png", width=480, height=480)
> ### Name: polygonChrom
> ### Title: Functions to plot circular chromosomes informations
> ### Aliases: polygonChrom linesChrom cPlotCircle chromPos2angle
> ### Keywords: hplot dplot
> 
> ### ** Examples
> 
> 
> 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)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>