splicegear (version 1.44.0)

plot.SpliceSitesGenomic: Function to plot SpliceSitesGenomic objects

Description

Function to plot SpliceSitesGenomic objects.

Usage

"plot"(x, col.variant = par("col"), col.exon = "white", split = FALSE, main = names(x@variants), ...)

Arguments

x

SpliceSitesGenomic-class

col.variant

a vector of colors for the different variants. The colors are recycled as necessary.

col.exon

a vector of colors for the exons. The colors are recycled as necessary.

split

split the plot of the variants in individual plots

main

character to use as a title. Recycled as necessary.

...

optional graphical parameters

Value

This function is used for its side-effect.

See Also

SpliceSitesGenomic-class

Examples

## a 10 bp window
seq.length <- as.integer(10)
## positions of the exons
spsiteIpos <- matrix(c(1, 3.5, 5, 9, 3, 4, 8, 10), nc=2)
## known variants
variants <- list(a=c(1,2,3,4), b=c(1,2,3), c=c(1,3,4))
##
n.exons <- nrow(spsiteIpos)

spvar <- new("SpliceSitesGenomic", spsiteIpos=spsiteIpos,
         variants=variants, seq.length=seq.length)

par(mfrow = c(3,1), mar = c(3.1, 2.1, 2.1, 1.1))

plot(spvar, split=TRUE, col.exon=rainbow(n.exons))