R: Plot a Multiple Sequence Alignment

plot.fasta {bio3d} | R Documentation

## Plot a Multiple Sequence Alignment

### Description

Produces a schematic representation of a multiple sequence alignment.

### Usage

    ## S3 method for class 'fasta'
    plot(x, hc = TRUE, labels = x$id, cex.lab = 0.7,
                             xlab = "Alignment index",
                             main = "Sequence Alignment Overview",
                             mar4 = 4, ...)

### Arguments

`x` | multiple sequence alignement of class ‘fasta’ as obtained from `seqaln`.
`hc` | logical, if TRUE plot a dendrogram on the left side. Alternatively, an object obtained from `hclust` can be provided.
`labels` | labels corresponding to each row in the alignment.
`cex.lab` | scaling factor for the labels.
`xlab` | label for x-axis.
`main` | a main title for the plot.
`mar4` | margin size for the labels.
`...` | additional arguments passed to function `hclust`.

### Details

`plot.fasta` is a utility function for producting a schematic representation of a multiple sequence alignment.

### Value

Called for its effect.

### Author(s)

Lars Skjaerven

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

### See Also

`seqaln`, `read.fasta`, `entropy`, `aln2html`.

### Examples

    # Read alignment
    aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))

    ## alignment plot
    plot(aln, labels=basename.pdb(aln$id))

    ## Works also for a 'pdbs' object
    attach(transducin)
    plot(pdbs)

    detach(transducin)

    ## Not run:
    infile <- "http://pfam.xfam.org/family/PF00071/alignment/seed/format?format=fasta"
    aln <- read.fasta( infile )
    plot(aln)

    ## End(Not run)

[Package bio3d version 2.4-2 Index]