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ape

image.DNAbin

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

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")

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24