Plot a Multiple Sequence Alignment

Produces a schematic representation of a multiple sequence alignment.

# S3 method for 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.

References

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

Author

Lars Skjaerven

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)

if (FALSE) {
infile <- "http://pfam.xfam.org/family/PF00071/alignment/seed/format?format=fasta"
aln <- read.fasta( infile )
plot(aln)
}