plot.fasta. bio3d 2.3-0

Usage

"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.

Description

Produces a schematic representation of a multiple sequence alignment.

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.

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)

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

Author

Lars Skjaerven

Plot a Multiple Sequence Alignment