Hive Plots in using Python & matplotlib!
pypi page: https://pypi.python.org/pypi/hiveplot
How to install hiveplot
hiveplot, you need to have
matplotlib installed - that's the only dependency required. If you are using
networkx to create your graphs, you will need that as well.
To run one of the notebook examples, you may need to install the Protein Interaction Network package from GitHub.
How to use hiveplot
Hive Plots are used for visualizing large network data in a rational way. Hive Plots are non-trivial to create, but I have made this Python package to help boil it down to the essentials.
The original creator of Hive Plots is Martin Krzywinski of the BCGSC. His website is at: http://mkweb.bcgsc.ca
An example graph is available in the
test folder. Alternatively, you can view the IPython notebook online: http://nbviewer.ipython.org/github/ericmjl/hiveplot/blob/master/test/Tests.ipynb
To start, I assume that you have some network data. In your network data, you will have nodes and edges.
Firstly, decide how you will group your nodes. Hive plots work best with up to 3 groups. Secondly, decide how you will order your nodes along each group. A common ordering is by degree centrality, which is how hiveplot currently does it automatically. Together, you can put together the first parameter put into hiveplot, which is a dictionary of
## assume that you have a graph called G nodes = dict() nodes['group1'] = [(n,d) for n, d in G.nodes(data=True) if d == some_criteria()] nodes['group2'] = [(n,d) for n, d in G.nodes(data=True) if d == other_criteria()] nodes['group3'] = [(n,d) for n, d in G.nodes(data=True) if d == third_criteria()]
You may wish to sort your nodes by some criteria.
for group, nodelist in nodes.items(): nodes[group] = sorted(nodelist, key=keyfunc()) ...
keyfunc() might work on the node attributes
d. That is why we included the
d dictionary of attributes inside.
Finally, you will need to get just the node ids out.
nodes[group] = [n for n, d in nodes[group]]
Next, you will need to group your edges. Do this in a similar fashion as nodes.
edges = dict() edges['group1'] = [(u,v,d) for u,v,d in G.edges(data=True) if d == some_criteria()] ...
Finally, you will need a color map for the nodes and edges respectively.
nodes_cmap = dict() nodes_cmap['group1'] = 'green' nodes_cmap['group2'] = 'red' nodes_cmap['group3'] = 'blue' edges_cmap = dict() edges_cmap['group1'] = 'green' ...
Once all of this is setup, you can plot the Hive Plot!
h = HivePlot(nodes, edges, nodes_camp, edges_cmap) h.draw()
All contributions to improve the package are welcome!
- Changed the setup script to use
- Fixed a bug that would cause drawing to not work on Python 3
dict_keyobjects do not have a
- Changed all tabs into four spaces.