bio3d (version 2.1-2)

plot.fasta: Plot a Multiple Sequence Alignment

Description

Produces a schematic representation of a multiple sequence alignment.

Usage

## S3 method for class 'fasta':
plot(x, plot.labels = TRUE,
                     plot.bars = TRUE,
                     plot.lines = FALSE,
                     plot.axis = TRUE,
                     seq.index = NULL,
                     color.conserved = FALSE,
                     cutoff=0.5, 
                     col=NULL,
                     bars.scale=2,
                     row.spacing=0.5,
                     aln.col="grey50",
                     cex.text=1, add=FALSE, ...)

Arguments

x

multiple sequence alignement of class fasta as obtained from seqaln.

plot.labels

logical, if TRUE labels will be printed next to the sequence bar.

plot.bars

logical, if TRUE an additional bar representing sequence conservation will be plotted.

plot.lines

logical, if TRUE sequence conservation will be represented with a plot.

plot.axis

logical, if TRUE x-axis will be plotted.

seq.index

printed tick labels will correspond to the sequence of the provided index.

color.conserved

logical, if TRUE conserved residues will be colored according to clustal coloring scheme.

cutoff

conservation cutoff value below which alignment columns are not colored.

col

character vector with color codes for the conservation bars. By default, heat.colors will be used.

bars.scale

scaling factor for the height of the conservation bar when plot.bars=TRUE.

row.spacing

space between the sequence bars.

aln.col

color of the alignment bars.

cex.text

scaling factor for the labels.

add

logical, if TRUE plot.new() will not be called.

...

additional arguments not paseed anywhere.

Value

• Called for its effect.

Details

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

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)

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