Create a HTML Page For a Given Alignment
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://thegrantlab.org/bio3d/>Bio3D</a>",
fontsize="11pt", bgcolor=TRUE, colorscheme="clustal")aln |
an alignment list object with |
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
|
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.
## 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.