rete: Network Analysis for Cell- and Systems Biology

HotNet2 Examples

We provide example config files for creating influence matrices, running simpleRun.py, as well as generating heat scores, delta selection, and running Hotnet2 with/without significance testing. Below we demonstrate how to run HotNet2 using these examples. Please consult the config files in example/configs to see the parameters used for each example.

All examples are located in the example/ directory. The example directory by default includes test data for running HotNet2 using mutation data or a heat file, as well as a test network.

First, you must create the influence matrix and directory of permtued influence matrices used by HotNet2 in these examples. To do so, run:

python makeRequiredPPRFiles.py @example/configs/influence_matrix.config

If you want to run the consensus procedure, you can create a second influence matrix and a directory of permuted influence matrices, you can run:

python makeRequiredPPRFiles.py @example/configs/influence_matrix2.config

To run the simpleRun example, execute:

python runHotNet2.py @example/configs/simple.config

This will run delta selection, HotNet2, and statistical significance testing using the heat file example/example.heat and store the output in example/output/simple. Because delta is selected using a permutation test, the output may vary slightly from run to run. You can see visualizations of the subnetworks in example/output/simple/viz, e.g.

As above, if you want to run the consensus procedure, you can also run the simpleRun example with the second influence matrix:

python runHotNet2.py @example/configs/simple2.config

To run an example using mutation data, consider the following steps:

Create an output directory.
```
mkdir example/output/mutation
```

Generate the heat file from the mutation data.

python generateHeat.py @example/configs/heat.config

Perform delta selection.

python bin/findThreshold.py @example/configs/delta.config

(Note that findThreshold.py will output a file that contains a distribution of deltas. In practice, you would use this distribution to choose the delta for running HotNet2 (e.g. by taking the median), and then update the delta parameter of example/configs/significance.config and example/configs/run.config)

Run HotNet2 (without significance testing).

python bin/findComponents.py @example/configs/run.config

Run HotNet2 (with significance testing).

python bin/findComponents.py @example/configs/significance.config

Make results website.

python bin/makeResultsWebsite.py @example/configs/website.config

Run consensus procedure.

python identifyConsensus.py @example/configs/consensus.config

Change to the directory of the visualization.

cd example/output/mutation/significance/viz

Start a web server for the visualzation.
```
python -m SimpleHTTPServer
```
In a browswer, load the webpage for the visualization.
```
http://localhost:8000
```