tablecode: to plot genetic code as in textbooks

In seqinr: Biological Sequences Retrieval and Analysis

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")

See Also

translate, syncodons

Examples

#
# Show me the standard genetic code:
#

 tablecode()

seqinr documentation built on May 29, 2024, 6:36 a.m.