aln2html: Create a HTML Page For a Given Alignment

In bio3d: Biological Structure Analysis

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 <a href=http://thegrantlab.org/bio3d/>Bio3D</a>",
         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.

Note

Your web browser should support style sheets.

Author(s)

Barry Grant

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")

## End(Not run)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.