plot.vhica | R Documentation |
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.
## S3 method for class 'vhica'
plot(x, sp1 = NULL, sp2 = NULL, ...)
x |
An object of class |
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 |
The resulting figure displays genes as circles, and transposable elements as symbols.
Implementation: Arnaud Le Rouzic <lerouzic@legs.cnrs-gif.fr>
Scientists who designed the method: Gabriel Wallau, Aurélie Hua-Van, Arnaud Le~Rouzic.
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.
read.vhica
, image.vhica
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)
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