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

Description Usage Arguments Details Author(s) References See Also Examples

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

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## S3 method for class '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.

Author(s)

Implementation: Arnaud Le Rouzic <lerouzic@legs.cnrs-gif.fr>
Scientists who designed the method: Gabriel Wallau, Aurélie Hua-Van, Arnaud Le~Rouzic.

References

Gabriel Luz Wallau, Arnaud Le Rouzic, Pierre Capy, Elgion Loreto, Aurélie Hua-Van. VHICA: A new method to discriminate between vertical and horizontal transposon transfer: application to the mariner family within Drosophila. Molecular biology and evolution 33 (4), 1094-1109.

See Also

read.vhica, image.vhica

Examples

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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)

Example output

Loading required package: ape

vhica documentation built on March 2, 2020, 5:07 p.m.