aln2html {bio3d} | R Documentation |
Renders a sequence alignment as coloured HTML suitable for viewing with a web browser.
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")
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. |
Called for its effect.
Your web browser should support style sheets.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
read.fasta
, write.fasta
, seqaln
## 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