aln2html {bio3d}R Documentation

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://mccammon.ucsd.edu/~bgrant/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

## Read an example alignment
aln <- read.fasta(system.file("examples/kinesin_xray.fa",package="bio3d"))

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


[Package bio3d version 1.0-6 Index]