Building an extension to DeMapper

Adding a new Mapper step

Mapper options and code is defined in code.mapper.mapper()

To add a new functionality for a step, you can easily make the switch-case to include your new Mapper. Make sure your code is well-tested and documented at the beginning of the file.

Adding a new Analysis type

Let’s take adding a new analysis type: “compute_modularity” as an example on how to add a new analysis type:

1. Create a new matlab function (as a file) that will be the entrypoint to your new analysis. In our example, create code/analysis/compute_modularity.m with the associated inputs, comments, and code:

   function compute modularity(res)
   % COMPUTE_MODULARITY Compute the modularity of the mapper shape graph
   % <detailed comments>
   ...
   <code>
   ...
   end
   

2. Make sure you test the functionality before you add it to the library. You can use one of the data fixtures in tests to verify your code. While in the process, create a test file. In our example, create tests/analysis/test_compute_modularity.m. Follow the similar test files in the same folder and make sure you use assert(..) to verify that a variable is correct.

3. Now that you are confident your code works, you can add it to the code.analysis.run_analysis() switch-case by adding a new case with your analysis type. For example:

   switch analysis.type
       case 'compute_modularity'
           ...
   end
   

4. Note: if you want to use information from the cohort file (TR value or task_path), check different examples in the run_analysis.m file and implement them within your case.

5. Test running from a json file by addind your new type as another analysis to be run in “analyses”. For example, add the line in the json file:

   { "type": "compute_modularity" }
   

   or

   { "type": "compute_modularity", "args": { ... } }
   

6. Run on your dataset and fine-tune as bugs might appear. Submit your code as a Pull-Request to the github repository and let other people know about your awesome analysis.