[Bioperl-l] Draw phylogenetic trees with bar chart

[Chris Bailey]

Florent Angly wrote:
> Dear Bioperl users,
>
> I need to represent graphically phylogenetic trees as cladograms or 
> phylograms using Perl. An additional requirement is that I would like 
> to add graph data as bar chart on top of it as in this example:
>    http://scums.sdsu.edu/Mapper/images/b.gif
>
> Now, I have read the BioPerl howto and know about the 
> Bio::TreeIO::svggraph and Bio::Tree::Draw::Cladogram modules. The 
> first one uses the SVG Perl module whereas the other one uses the 
> PostScript module to create EPS images. I do not know why there are 2 
> very similar modules to draw trees (in different locations), but none 
> of them seem to able to plot additional information on the tree.
I'm not aware of any inbuilt code in any of  these modules to do what 
you're asking. In the past, the way I've added extra information into 
trees is as follows:
1) Embed the data you want to graph into the alignment/tree file, such 
that when the tree is drawn, for example, the length of the bar you want 
drawn is part of the text on the tree node in question
2) Draw the tree as an SVG image using Bio::TreeIO.
3) Parse the SVG document using your XML parser of choice (I've used 
XML::Simple for this in the past)
4) extract all the <text> elements and their CDATA.
5) the text element will contain an x and y co-ordinate and the CDATA 
will contain the text string itself
6) pull out the data you need to draw the graph (the information you 
added in 1) using regexps etc.
7) add an element to the SVG document (e.g. <rect x="80" y="500" 
height="10" width="125" style="fill:blue" />) simply change the x and y 
to match the coordinates of the text element (+ an offset to get 
everything looking right), and change width to the value you extracted 
in (6)
8) repeat steps 5 to 7 for all the text elements in your SVG document
9) output new SVG document to a file
10) ????
11) Profit

This pattern will also work for more complex data, since you can always 
add more data to each text node, and it's more than possible to generate 
any type of chart data you like with the right combination of shape 
primitives.

Cheers,

Chris
>
> Is there any other Perl code that you know of that would facilitate 
> doing what I want to do? If not, how should I modify one of the 2 
> mentioned BioPerl modules to plot bar charts, and which one??
>
> Thanks,
>
> Florent
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-- 
-----------------------
Chris Bailey
Centre for Systems Biology
School of Biosciences
University of Birmingham
Edgbaston, Birmingham, B15 2TT
United Kingdom
T: +44(0)121 414 8849
E: c.bailey at bham.ac.uk