Beefy Boxes and Bandwidth Generously Provided by pair Networks
Don't ask to ask, just ask
 
PerlMonks  

Re: supertree construction in perl

by pvaldes (Chaplain)
on Oct 09, 2012 at 09:00 UTC ( #997955=note: print w/replies, xml ) Need Help??


in reply to supertree construction in perl

If you want to play with the nodes, calculate bootstrap values etc, start with bioperl

But if you want only to plot a nice tree with few nodes and non interactive, you have at least two superb options outside perl. Each time I see the plot that you want to make, something in my mind is whispering at me: this is clearly either a graphviz job...

use graphviz; my $plot = GraphViz->new( layout => 'dot', directed => 0, rankdir => 'TB' ); # dot = directed plot as output, # better than 'neato' for drawing trees

... or either a work for the ever elegant latex

use LaTeX::Driver;

(\usepackage{tikz}). Both can produce the plot that you want, after perl massage and pass the data in an accurate way. Of these, Latex is probably the only that can plot _exactly_ what you show in the picture, but don't underestimate graphviz, it is a solid and very powerful program

And if you have a big structure with many thousands or millions of nodes to plot, R is your man. Graphviz is not designed for this kind of situation.

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://997955]
help
Chatterbox?
erix just did a 12 km-run. Slow, but unstoppable!
[choroba]: My recent record is 10km in 1 hour :)
[perldigious]: Nice erix... perldigious' legs are so sore from portaging his kayak from place to place last weekend he can barely hobble 12m. :-)
[erix]: you're faster than me then :)
[erix]: well, at the moment, that is :)
[erix]: I should lose some weight although I keep telling myself that I'm doing extra training by lugging it along
[erix]: I saw a common kingfisher and a couple of bullfinches

How do I use this? | Other CB clients
Other Users?
Others chanting in the Monastery: (9)
As of 2017-05-24 12:42 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?