Plot a Multiple Sequence Alignment
Produces a schematic representation of a multiple sequence alignment.
## S3 method for class 'fasta'
plot(x, hc = TRUE, labels = x$id, cex.lab = 0.7,
xlab = "Alignment index",
main = "Sequence Alignment Overview",
mar4 = 4, ...)x |
multiple sequence alignement of class ‘fasta’ as
obtained from |
hc |
logical, if TRUE plot a dendrogram on the left
side. Alternatively, an object obtained from |
labels |
labels corresponding to each row in the alignment. |
cex.lab |
scaling factor for the labels. |
xlab |
label for x-axis. |
main |
a main title for the plot. |
mar4 |
margin size for the labels. |
... |
additional arguments passed to function |
plot.fasta is a utility function for producting a schematic
representation of a multiple sequence alignment.
Called for its effect.
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
# Read alignment
aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))
## alignment plot
plot(aln, labels=basename.pdb(aln$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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.