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.)

There's 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 subprocesssubprocess.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.

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