Create a HTML Page For a Given Alignment

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.

Description

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

Value

Called for its effect.

References

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

Note

Your web browser should support style sheets.

Examples

## 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")

See also

read.fasta, write.fasta, seqaln

Author

Barry Grant