For Developers

NLA allows for adding custom tests to the codebase

Creating additional edge-level tests

Current tests are located in +nla/+edge/+test. This is also where any user-created custom tests will need to be saved. All edge-level test objects must inherit from nla.edge.BaseTest

• Test object

• Result object

  A result object must be defined for the test edge-level results. If no custom data fields are needed, then the object in +nla/+edge/+result/Base.m may be used and this step can be skipped. If a new result is needed, a permutation result inheriting +nla/+edge/+result/PermBase must also be created

  class edge.result.Base

  Base class of results of edge-level analysis

  Parameters:

  • size – The size of the Trimatrix being analyzed

  • prob_max – The threshold for the p-value

  output(net_atlas, flags, prob_label)

  Plotting method for the edge-level analysis results

  Parameters:

  • net_atlas – The network atlas of the data

  • flags – Options from the front-end for plotting

  • prob_label – Extra information appended to title of plot

Creating additional network-level tests

All custom created tests must be saved in +nla/+net/+test; the tests present can also be used as templates. All network-level results must fit into the NetworkTestResult object.

Since these tests are all different with different results and statistics, there is no base test to inherit. The only requirements are below

• Constant properties required

  properties (Constant)
    name = "students_t"
    display_name = "Student's T-test"
    statistics = ["t_statistic", "single_sample_t_statistic"]
    ranking_statistic = "t_statistic"
  end
  

  name:

  The name of the test with no special characters (spaces, &, etc)

  display_name:

  A formal name that will be used for displaying in the GUI. Any string will work

  statistics:

  All statistics that will be generated by the test. No special characters

  ranking_statistic:

  The statistic used for ranking and calculating p-values. Note: if there is a single sample version of the statistic in addition to a two-sample statistic, the GUI will automatically add “single_sample_” during rankings for non-permuted and within network pair ranking.

• A run method

  result = run(obj, test_options, edge_test_results, network_atlas, permutations)
  

  test_options:

  Also called input_struct in edge-level tests. Parameters needed to run the test.

  edge_test_results:

  The output from the edge-level test.

  network_atlas:

  A network atlas of the form nla.NetworkAtlas

  permutations:

  Boolean to determine if the test is being run with permutations (true) or without (false)

  result:

  NetworkTestResult

• requiredInputs See Edge-level tests