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

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)
}