seqinr: tablecode – R documentation

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tablecode

to plot genetic code as in textbooks

Description

This function plots a genetic code table as in textbooks, that is following the order T > C > A > G so that synonymous codons are almost always in the same boxes.

Usage

tablecode(numcode = 1, urn.rna = s2c("TCAG"), dia = FALSE, latexfile = NULL,
label = latexfile, size = "normalsize", caption = NULL,
preaa = rep("", 64), postaa = rep("", 64), 
precodon = preaa, postcodon = postaa)

Arguments

`numcode`	The genetic code number as in `translate`
`urn.rna`	The letters to display codons, use s2c("UCAG") if you want the code in terms of RNA sequence
`latexfile`	The name of a LaTex file if you want to redirect the output
`label`	The label for the LaTeX table
`size`	The LaTex size of characters for the LaTeX table
`preaa`	A string to insert before the amino-acid in the LaTeX table
`postaa`	A string to insert after the amino-acid in the LaTeX table
`precodon`	A string to insert before the codon in the LaTeX table
`postcodon`	A string to insert after the codon in the LaTeX table
`caption`	The caption of the LaTeX table
`dia`	to produce a yellow/blue plot for slides

Details

The codon order for preaa, postaa, precodon, and postcodon should be the same as in paste(paste(rep(s2c("tcag"), each =16), s2c("tcag"), sep = ""), rep(s2c("tcag"), each = 4), sep = "")

Author(s)

J.R. Lobry

References

citation("seqinr")

Examples

#
# Show me the standard genetic code:
#

 tablecode()

seqinr

Biological Sequences Retrieval and Analysis

v4.2-16

GPL (>= 2)

Authors

Delphine Charif [aut], Olivier Clerc [ctb], Carolin Frank [ctb], Jean R. Lobry [aut, cph], Anamaria Necşulea [ctb], Leonor Palmeira [ctb], Simon Penel [cre], Guy Perrière [ctb]

Initial release

2022-05-19