plot.fasta {bio3d}

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)