Visualization
We provide two scripts for generating an interactive web application for viewing and exploring the exclusive sets enumerated by compute_exclusivity.py. Below, we describe the usage of the scripts, and then demonstrate an example.
After enumerating sets with compute_exclusivity.py, run viz/generate_viz_data.py with the following arguments to generate the JSON files used by the web sever:
| Argument | Required (Default) | Description |
|---|---|---|
| -mf/--mutation_file | True | Path to mutation file generated by process_mutations.py. |
| -rf/--results_files | True | Path to output files generated by compute_exclusivity.py. |
| -o/--output_file | True | Path to output file in JSON format. |
| -wf/--weights_file | True | Path to weights file in Numpy format generated by compute_mutation_probabilities.py. |
| -N/--num_sets | False (1000) | Restrict the number of sets included per result file. The output will include the union of all such sets. |
| -h/--help | False | Display usage instructions. |
| -v/--verbose | False (0) | Choices: 0, 1, 2, 3, 4, 5. Higher values correspond to more verbose output. |
For performance, we recommend only viewing a few thousand sets in the browser. You can control the number of sets with the -N argument.
After generating the visualization JSON files, run server.py with the following arguments:
| Argument | Required (Default) | Description |
|---|---|---|
| -i/--input_files | True | Path to JSON files generated by generate_viz_data.py. |
| -r/--run_names | True | Short (one word) names for each of the JSON files. |
| -p/--port | False (8000) |
Port used by the web server. |
| -h/--help | False | Display usage instructions. |
In this example, we view the output of two runs on the colorectal and endometrial data.
First, run the web server on the two JSON files we generated with viz/generate_viz_data.py:
python viz/server.py -i data/coadread-triple-viz.json data/ucec-triple-viz.json -r COADREAD UCEC
Then point your browser to http://localhost:8000. There are two key features on the page.
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A paginated table, listing the exclusive sets. You can search, sort, or filter the rows or columns in the table, and switch between viewing the p-values, FDRs, or runtimes using the tabs at the top.
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Click on a row in the table to view the corresponding rows in the mutation matrix A and the mutation probability matrix P.
Last modified: 9:46 PM Monday, May 9, 2016 (EDT)