dotchart.uco {seqinr} | R Documentation |
Draw a Cleveland dot plot for codon usage tables
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, ...)
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 |
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 |
J.R. Lobry
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.
# 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)