dotchart.uco: Cleveland plot for codon usage tables

In seqinr: Biological Sequences Retrieval and Analysis

Cleveland plot for codon usage tables

Description

Draw a Cleveland dot plot for codon usage tables

Usage

dotchart.uco(x, numcode = 1, aa3 = TRUE, pt.cex = 0.7, alphabet =
                 s2c("tcag"), pch = 21, gpch = 20, bg = par("bg"), cex
                 = 0.7, color = "black", gcolor = "black", lcolor =
                 grey(0.9), xlim, offset = 0.4, ...)

Arguments

x	table of codon usage as computed by uco.
numcode	the number of the code to be used by translate.
aa3	logical. If TRUE use the three-letter code for amino- acids. If FALSE use the one-letter code for amino-acids.
pt.cex	the character size to be used for points.
alphabet	character for codons labels
pch	the plotting character or symbol to be used.
gpch	the plotting character or symbol to be used for group values.
bg	the background color to be used.
cex	the character expansion size passed to dotchart.
color	the color(s) to be used for points an labels.
gcolor	the single color to be used for group labels and values.
lcolor	the color(s) to be used for the horizontal lines.
xlim	horizontal range for the plot
offset	offset in inches of ylab and labels; was hardwired to 0.4 before R 4.0.0
...	graphical parameters can also be specified as arguments

Value

An invisible list with components:

x	table of codon usage
labels	codon names
groups	amino acid factor
gdata	sums by amino acid
ypg	the y-axis coordinates for amino acids
ypi	the y-axis coordinates for codons

Author(s)

J.R. Lobry

References

Cleveland, W. S. (1985) The Elements of Graphing Data. Monterey, CA: Wadsworth. citation("seqinr")

See Also

dotchart, uco, aaa, translate

Examples

# Load dataset:
data(ec999)
# Compute codon usage for all coding sequences:
ec999.uco <- lapply(ec999, uco, index="eff")
# Put it in a dataframe:
df <- as.data.frame(lapply(ec999.uco, as.vector))
# Add codon names:
row.names(df) <- names(ec999.uco[[1]])
# Compute global codon usage:
global <- rowSums(df)
# Choose a title for the graph:
title <- "Codon usage in 999 E. coli coding sequences"
# Plot data:
dotchart.uco(global, main = title)

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