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
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