seqinr (version 1.0-1)

dotchart.uco: Cleveland plot for codon usage tables

Description

Draw a Cleveland dot plot for codon usage tables

Usage

dotchart.uco(x, numcode = 1, aa3 = TRUE, cex = 0.7, alphabet = s2c("tcag"),
 pch = 21, gpch = 20, bg = par("bg"), color = par("fg"), gcolor = par("fg"),
lcolor = "gray", xlim, ...)

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.

cex

the character size to be used.

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.

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

...

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

References

Cleveland, W. S. (1985) The Elements of Graphing Data. Monterey, CA: Wadsworth. To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.

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)