R: Plot of DNA Sequence Alignement

image.DNAbin {ape} | R Documentation

## Plot of DNA Sequence Alignement

### Description

This function plots an image of an alignment of nucleotide sequences.

### Usage

    ## S3 method for class 'DNAbin'
    image(x, what, col, bg = "white", xlab = "", ylab = "",
          show.labels = TRUE, cex.lab = 1, legend = TRUE,
          grid = FALSE, show.bases = FALSE, base.cex = 1,
          base.font = 1, base.col = "black", ...)

### Arguments

`x` | a matrix of DNA sequences (class `"DNAbin"`).
`what` | a vector of characters specifying the bases to visualize. If missing, this is set to “a”, “g”, “c”, “t”, “n”, and “-” (in this order).
`col` | a vector of colours. If missing, this is set to “red”, “yellow”, “green”, “blue”, “grey”, and “black”. If it is shorter (or longer) than `what`, it is recycled (or shortened).
`bg` | the colour used for nucleotides whose base is not among `what`.
`xlab` | the label for the x-axis; none by default.
`ylab` | Idem for the y-axis. Note that by default, the labels of the sequences are printed on the y-axis (see next option).
`show.labels` | a logical controlling whether the sequence labels are printed (`TRUE` by default).
`cex.lab` | a single numeric controlling the size of the sequence labels. Use `cex.axis` to control the size of the annotations on the x-axis.
`legend` | a logical controlling whether the legend is plotted (`TRUE` by default).
`grid` | a logical controlling whether to draw a grid (`FALSE` by default).
`show.bases` | a logical controlling whether to show the base symbols (`FALSE` by default).
`base.cex, base.font, base.col` | control the aspect of the base symbols (ignored if the previous is `FALSE`).
`...` | further arguments passed to `image.default` (e.g., `xlab`, `cex.axis`).

### Details

The idea of this function is to allow flexible plotting and colouring of a nucleotide alignment. By default, the most common bases (a, g, c, t, and n) and alignment gap are plotted using a standard colour scheme.

It is possible to plot only one base specified as `what` with a chosen colour: this might be useful to check, for instance, the distribution of alignment gaps (`image(x, "-")`) or missing data (see examples).

### Author(s)

Emmanuel Paradis

### See Also

`DNAbin`, `del.gaps`, `alex`, `alview`, `all.equal.DNAbin`, `clustal`, `grid`, `image.AAbin`

### Examples

    data(woodmouse)
    image(woodmouse)
    rug(seg.sites(woodmouse), -0.02, 3, 1)
    image(woodmouse, "n", "blue") # show missing data
    image(woodmouse, c("g", "c"), "green") # G+C
    par(mfcol = c(2, 2))
    ### barcoding style:
    for (x in c("a", "g", "c", "t"))
        image(woodmouse, x, "black", cex.lab = 0.5, cex.axis = 0.7)
    par(mfcol = c(1, 1))
    ### zoom on a portion of the data:
    image(woodmouse[11:15, 1:50], c("a", "n"), c("blue", "grey"))
    grid(50, 5, col = "black")
    ### see the guanines on a black background:
    image(woodmouse, "g", "yellow", "black")

[Package ape version 5.4 Index]