vhica (version 0.2.4)

plot.vhica: Plots a VHICA regression between two species.

Description

The VHICA method is based on a contrast between gene divergence and codon usage bias. A regression between divergence and codon usage provides a reference, and sequences of interest (typically, transposable elements) will be compared to the reference genes.

Usage

# S3 method for vhica
plot(x, sp1 = NULL, sp2 = NULL, ...)

Arguments

x

An object of class vhica, created by read.vhica.

sp1

Name of the first species, as in the data files.

sp2

Name of the second species, as in the data files.

…

Additional options for plot.

Details

The resulting figure displays genes as circles, and transposable elements as symbols.

References

Gabriel Luz Wallau, Arnaud Le Rouzic, Pierre Capy, Elgion Loreto, Aur<U+00E9>lie Hua-Van. VHICA: A new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila. in prep.

See Also

read.vhica, image.vhica

Examples

# NOT RUN {
file.cb <- system.file("extdata", "mini-cbias.txt", package="vhica")
file.div <- system.file("extdata", "mini-div.txt", package="vhica")
file.tree <- if(require("ape")) system.file("extdata", "phylo.nwk", package="vhica") else NULL
vc <- read.vhica(cb.filename=file.cb, div.filename=file.div)
plot(vc, "dere", "dana")
image(vc, "mellifera:6", treefile=file.tree, skip.void=TRUE)
# }