Part 5: Graph Visualization
This section of the tutorial requires two dependencies that are outside OAK.
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/.
You can use
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
TODO: use test_obograph_utils for example