R: Cleveland plot for codon usage tables

dotchart.uco {seqinr} | R Documentation

## 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, ...)

### 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
`...` | 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)

[Package seqinr version 3.4-5 Index]