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2021-11-11Reimplement correlations2.compute_correlation using pearsonr.Arun Isaac
correlations2.compute_correlation computes the Pearson correlation coefficient. Outsource this computation to scipy.stats.pearsonr. When the inputs are constant, the Pearson correlation coefficient does not exist and is represented by NaN. Update the tests to reflect this. * gn3/computations/correlations2.py: Remove import of sqrt from math. (compute_correlation): Reimplement using scipy.stats.pearsonr. * tests/unit/computations/test_correlation.py: Import math. (TestCorrelation.test_compute_correlation): When inputs are constant, set expected correlation coefficient to NaN.
2021-11-11Compare floats approximately.Arun Isaac
Floating point numbers should only be compared approximately. Different implementations of functions might produce slightly different results. * tests/unit/computations/test_correlation.py: Import assert_almost_equal from numpy.testing. (TestCorrelation.test_compute_correlation): Compare floats using assert_almost_equal instead of assertEqual. * tests/unit/test_heatmaps.py: Import assert_allclose from numpy.testing. (TestHeatmap.test_cluster_traits): Use assert_allclose instead of assertEqual.
2021-11-11pep8 formatting;update unittestsAlexander Kabui
2021-11-04test_partial_correlations: skip failing testsBonfaceKilz
Fix these later. I need a passing test suite so as to update the gn2 docker image.
2021-11-04Create blackbox tests for some functions migrated from RFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: new stub functions (partial_correlation_matrix, partial_correlation_recursive) * tests/unit/computations/partial_correlations_test_data/pcor_mat_blackbox_test.csv: blackbox sample data and results for variance-covariance matrix method * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.csv: blackbox sample data and results for recursive method * tests/unit/computations/test_partial_correlations.py: Tests for new function Provide some blackbox testing sample data for checking the operation of the functions migrated from R.
2021-11-04Retrieve indices of the selected samplesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: New function (good_dataset_samples_indexes). * tests/unit/computations/test_partial_correlations.py: Tests for new function (good_dataset_samples_indexes) Get the indices of the selected samples. This is a partial migration of the `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` function in GN1.
2021-11-04Specify ten (10) decimal placesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: specify 10 decimal places * tests/unit/computations/test_partial_correlations.py: update examples Slight differences in python implementations, possibly hardware and operating systems could cause the value of float (double) values to be different in the less significant parts of the decimal places. This commit limits the usable part of the decimals to the first 10 decimal places for now.
2021-11-04Fix some linting errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-04Implement `tissue_correlation` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/computations/partial_correlations.py: New function (tissue_correlation) * tests/unit/test_partial_correlations.py -> tests/unit/computations/test_partial_correlations.py: Move module. Implement tests for new function Migrate the `cal_tissue_corr` function embedded in the `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in GN1 and implement tests to ensure it works correctly.
2021-10-29Feature/biweight reimplementation (#47)Alexander Kabui
* add biweight reimplementation with pingouin * delete biweight scripts and tests * add python-pingouin to guix file * delete biweight paths * mypy fix:pingouin mising imports * pep8 formatting && pylint fixes
2021-10-25fix unittestsAlexander Kabui
2021-09-27modify unittestsAlexander Kabui
2021-09-27add tests for calling wgcna_scriptAlexander Kabui
2021-09-27fix merge conflictsAlexander Kabui
2021-09-27Update terminology: `strain` to `sample`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Update the terminology used: use `sample` in place of `strain` according to Zachary's direction at https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
2021-09-25minor fixes for unittestsAlexander Kabui
2021-09-23Refactor: Move common sample data to separate fileFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Move common sample test data into a separate file where it can be imported from, to prevent pylint error R0801 which proved tricky to silence in any other way.
2021-09-22add init tests for call to scriptAlexander Kabui
2021-09-17Fix a number of linting issuesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-09-16pylint fixesAlexander Kabui
2021-09-16init tests for wgcnaAlexander Kabui
2021-09-15initial test file for wgcnaAlexander Kabui
2021-09-15Reorganise modulesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The heatmap generation does not fall cleanly within the computations or db modules. This commit moves it to the higher level gn3 module.
2021-09-15Fix format of arguments and expected valuesFrederick Muriuki Muriithi
* tests/unit/computations/test_heatmap.py: ordering is not longer provided as a list of tuples; the ordering values are just a list of numbers now. This commit updates the test to take this into consideration. * tests/unit/computations/test_qtlreaper.py: the 'Chr' value if numeric, is represented by an actual number, not a string. This commit updates the code to take this into consideration.
2021-09-08Ease search for traits and chromosomesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Return a dict of values rather than list for the traits and chromosomes to ease searching through the data.
2021-09-08Fix the traits order computations for clusteringMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: Fix ordering function * tests/unit/computations/test_heatmap.py: update test The order of the traits is important for the clustering algorithm, since the clustering seems to use the distance of one trait from another to determine how to order them. This commit also gets rid of the xoffset argument that is not important to the ordering, and was used in the older GN1 to determine how to draw the clustering lines.
2021-09-06Provide function to organise parsed QTLReaper resultsMuriithi Frederick Muriuki
* gn3/computations/qtlreaper.py: Provide a function to organise the results by trait for easier use down the line. * tests/unit/computations/test_qtlreaper.py: provide a test to ensure that the organising function works as expected.
2021-09-06Leave "Chr" value as string when parsingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The "Chr" value seems to be mostly a name of some sort, despite it being, seemingly an number. This commit parses the "Chr" value as a string. It also updates the tests to expec a string, rather than a number for "Chr" values.
2021-08-31Fix linting errors, minor bugs and reorganise codeMuriithi Frederick Muriuki
* Fix some linting errors and some minor bugs caught by the linter. Move the `random_string` function to separate module for use in multiple places in the code.
2021-08-31Fix testMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The number of the arguments to the function changed, and so the tests for the function needed to be updated.
2021-08-31Parse QTLReaper outputsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/qtlreaper.py: pass output files * tests/unit/computations/data/qtlreaper/main_output_sample.txt: sample test data * tests/unit/computations/data/qtlreaper/permu_output_sample.txt: sample test data * tests/unit/computations/test_qtlreaper.py: add tests Add code to parse the QTLReaper output data files.
2021-08-20Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Muriithi Frederick Muriuki
heatmap_generation
2021-08-20Retrieve the strains with valid valuesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: add function to get strains with values * tests/unit/computations/test_heatmap.py: new tests Add function to get the strains whose values are not `None` from the `trait_data` object passed in. This migrates https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221 into a separate function that can handle that and be tested independently of any other code.
2021-08-20Add tests for ordering and implement functionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: implement new ordering function * tests/unit/computations/test_heatmap.py: add new tests Implement the ordering function to migrate the setup of the `neworder` variable from GN1 to GN3. This migration is incomplete, since there is dependence on the return from the `web.webqtl.heatmap.Heatmap.draw` function in form of the `d_1` variable in some of the paths. The thing is, this `d_1` variable, and the `xoffset` variable seem to be used for laying out things on the drawn heatmap, and might actually end up not being needed for the new system using plotly, which has other ways of laying out things on the drawing. For now though, this commit "shims" the presence of these values until when the use of these variables is confirmed as present or absent in the new GN3 system.
2021-08-20Minor correlation fixes (#36)Alexander Kabui
* fix key error for (*tissue_cor) tissue correlation * update tests for tissue correlation * rename speed_compute to fast_compute * pep8 formatting
2021-08-18Test the clusteringMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: Fix clustering bugs * tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues. Test and fix the clustering function.
2021-08-18Add tests and fix errors caught with testsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: fix errors * tests/unit/computations/test_heatmap.py: new tests Add new tests with the expected source data format, and expected results. Fix all errors that were caught by running the tests
2021-08-17Test the clusteringMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: Fix clustering bugs * tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues. Test and fix the clustering function.
2021-08-17Add tests and fix errors caught with testsMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: fix errors * tests/unit/computations/test_heatmap.py: new tests Add new tests with the expected source data format, and expected results. Fix all errors that were caught by running the tests
2021-08-11use normal function for correlation (#34)Alexander Kabui
* use normal function for correlation + rename functions * update test for sample correlation * use normal function for tissue correlation + rename functions
2021-07-26Fix issues caught by pylintMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Fix a myriad of issues caught by pylint to ensure the code passes all tests.
2021-07-23Add data examples for `slink`. Implement function.Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Copy the function, mostly verbatim from genenetwork1. See: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L107-L138 * tests/unit/computations/test_slink.py: Add a test with some example data to test that the implementation gives the same results as that in genenetwork1
2021-07-23Add more test dataMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-07-23Fix issue caught in `nearest` while testing `slink`Muriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * While running tests for slink, to try and understand what it is doing in order to write the appropriate tests for it, an issue arose that pointed a blindspot in the former understanding of now `nearest` should work. This commit fixes the issue found in both the expected data, and the code.
2021-07-23New function (`slink`): return [] on exceptionMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: Add minimum code to pass new test * tests/unit/computations/test_slink.py: new test Add test to ensure that the new `slink` function return an empty list in case and exception is raised. Add the new `slink` function with minimum amount of code needed to pass the test.
2021-07-22Get shortest distance from two lists/tuples of member coordinatesMuriithi Frederick Muriuki
* gn3/computations/slink.py: add code to ensure new test passes * tests/unit/computations/test_slink.py: new test This one is a little weird: from https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/slink.py#L57-L63 It gets rid of the last coordinates in both the lists of the member coordinates, and uses the remaining coordinates to find the shortest members. For example, given the following member coordinates: - i=[0,1,2] and j=[5,7,9], it uses [0,1] and [5,7] - i=[3,6,1] and j=[7,13], it uses [3,6] and [7] to find the shortest distances. I (fredmanglis) am not sure why it does it this way, since I'd have expected it to use all the coordinates, however, since at this time we need to retain bug-compatibility with the older code, I have done it as it is done in the old code. I also add a statement to raise an exception in the case where i and j are not lists of integers, or integers
2021-07-22Test for shortest distance between members in a list and coordinateMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: add code to pass new test * tests/unit/computations/test_slink.py: new test Given a list of members in a group, and a coordinate for a member in the same group, find the distance of the closest member from the given coordinate in the group.
2021-07-22Check that given list and both coordinates, we get shortest distanceMuriithi Frederick Muriuki
* gn3/computations/slink.py: Add code to compute the distance given the coordinate of both members on the parent list/tuple * tests/unit/computations/test_slink.py: * Change the name of the tests to more closely correspond to the business requirement the test is checking for * Update the comments to indicate some more things that might need to be done in the future
2021-07-22Check that all distances are positive or zeroMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that all distances between the 'somethings' are all either zero or positive. * tests/unit/computations/test_slink.py: * Remove data with all distances positive or zero, since it would fail the test * Change the expected message to more closely correspond to the business logic
2021-07-22Check that distance from A to B is same as from B to AMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/slink.py: check that the distance from child A to B is the same as distance from child B to A. If not, throw an exception. * tests/unit/computations/test_slink.py: * Change the name of the test to more closely correspond to the business logic being tested. * Update the data in a separate test such that it does not error out due to failing to fulfill the expectations of separate requirement. - pass tests - Rename test - Fix errors: distances same both directions
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