bio3d (version 2.3-4)

aln2html: Create a HTML Page For a Given Alignment

Description

Renders a sequence alignment as coloured HTML suitable for viewing with a web browser.

Usage

aln2html(aln, file="alignment.html", Entropy=0.5, append=TRUE,
         caption.css="color: gray; font-size: 9pt",
         caption="Produced by Bio3D",
         fontsize="11pt", bgcolor=TRUE, colorscheme="clustal")

Arguments

aln

an alignment list object with id and ali components, similar to that generated by read.fasta.

file

name of output html file.

Entropy

conservation ‘cuttoff’ value below which alignment columns are not coloured.

append

logical, if TRUE output will be appended to file; otherwise, it will overwrite the contents of file.

caption.css

a character string of css options for rendering ‘caption’ text.

caption

a character string of text to act as a caption.

fontsize

the font size for alignment characters.

bgcolor

background colour.

colorscheme

conservation colouring scheme, currently only “clustal” is supported with alternative arguments resulting in an entropy shaded alignment.

Value

Called for its effect.

References

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

See Also

read.fasta, write.fasta, seqaln

Examples

# NOT RUN {
## Read an example alignment
aln <- read.fasta(system.file("examples/hivp_xray.fa",package="bio3d"))

## Produce a HTML file for this alignment
aln2html(aln, append=FALSE, file=file.path("eg.html"))
aln2html(aln, colorscheme="ent", file="eg.html")
## View/open the file in your web browser
#browseURL("eg.html")
# }