Part 5: Graph Visualization

This section of the tutorial requires two dependencies that are outside OAK.

  • Graphviz

  • OBOGraphViz

Install Graphviz

Graphviz is an open-source graph visualization software that provides a way to represent information about graphs and networks.

For installation refer to Graphviz.org/download/.

Install OBOGraphViz

OBOGraphViz is a Javascript package that allows you to visualize OBOGraphs using Graphviz.

You can use npm or yarn to install the OBOGraphViz package.

npm install obographviz

Command Line Usage

Using OAK, you can generate graph visualizations directly from the command line as follows:

runoak -i obolibrary:fbbt.obo viz FBbt:00004751 -p i,p -o wing-vein.png

Then open the file wing-vein.png using a tool such as Preview, or in a web browser.

If you omit the -o/--output option then the png will be written to a temp file and immediately opened:

runoak -i obolibrary:fbbt.obo viz FBbt:00004751 -p i,p

How this works

  • First, the OboGraphInterface is invoked to query all ancestors of the term

  • in this case the implementation is pronto plus graph walking code

  • after an obograph is generated this is passed to the obographviz library

Programmatic usage

TODO: use test_obograph_utils for example