plot – Tree plotting in Python

plot – Tree plotting in Python

I develop ETE, which is a python package intended, among other stuff, for programmatic tree rendering and visualization. You can create your own layout functions and produce custom tree images:

It has a focus on phylogenetics, but it can actually deal with any type of hierarchical tree (clustering, decision trees, etc.)

Theres graphviz – http://www.graphviz.org/. It uses the DOT language to plot graphs. You can either generate the DOT code yourself, or use pydot – https://github.com/pydot/pydot. You could also use networkx – http://networkx.lanl.gov/tutorial/tutorial.html#drawing-graphs, which make it easy to draw to either graphviz or matplotlib.

networkx + matplotlib + graphviz gives you the most flexibility and power, but you need to install a lot.

If you want a quick solution, try:

Install Graphviz.

open(hello.dot,w).write(digraph G {Hello->World})
import subprocess
subprocess.call([path/to/dot.exe,-Tpng,hello.dot,-o,graph1.png]) 
# I think this is right - try it form the command line to debug

Then you install pydot, because pydot already does this for you. Then you can use networkx to drive pydot.

plot – Tree plotting in Python

For basic visualization I would consider using treelib,

It is very straightforward and easy to use:

 from treelib import Node, Tree

 tree = Tree()

 tree.create_node(Harry, harry)  # No parent means its the root node
 tree.create_node(Jane,  jane   , parent=harry)
 tree.create_node(Bill,  bill   , parent=harry)
 tree.create_node(Diane, diane  , parent=jane)
 tree.create_node(Mary,  mary   , parent=diane)
 tree.create_node(Mark,  mark   , parent=jane)

 tree.show()

Output:

Harry
├── Bill
└── Jane
    ├── Diane
    │   └── Mary
    └── Mark