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2021-11-12Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-11-12Pass in parser function for flexibilityFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * To improve the usefulness of already existing code, provide the parser function as an argument to the `parse_input_line` function. This was found to be useful when writing code to compare the `pcor.test` function in GN1 and the `pingouin.partial_corr` function. The format of the data generated when getting results for the `pcor.test` function shared a lot with that of the `pcor.rec` function, but it was different in a few, places, and the differences were non-trivial, needing different parsing processes. In such a case, it was found necessary to just pass in the function to do the actual parsing, rather than create code with the same form as the existing one, save for the function being called.
2021-11-11Remove redundant check on the Pearson correlation coefficient.Arun Isaac
The Pearson correlation coefficient always has a value between -1 and 1. So, this check is redundant. * gn3/heatmaps.py (cluster_traits.__compute_corr): Remove redundant check on the Pearson correlation coefficient.
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.
2021-11-11Reimplement __items_with_values using list comprehension.Arun Isaac
* gn3/computations/correlations2.py: Remove import of reduce from functools. (__items_with_values): Reimplement using list comprehension.
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
2021-11-11pylint fixes and pep8 formattingAlexander Kabui
2021-11-11fix target and base sample data orderAlexander Kabui
2021-11-11fix:spawned processes memory issuesAlexander Kabui
2021-11-11replace list with generatorsAlexander Kabui
2021-11-11Disuse absolute paths to guix.Arun Isaac
It is safe to assume that the user has correctly set up guix in their PATH. * README.md: Disuse absolute paths to guix in command invocations.
2021-11-11Disuse GUIX_PACKAGE_PATH.Arun Isaac
guix-bioinformatics is a Guix channel that is set up by `guix pull'. There is no need to specify it explicitly using GUIX_PACKAGE_PATH. * README.md: Do not explicitly set GUIX_PACKAGE_PATH for any command.
2021-11-11Update PULL_REQUEST_TEMPLATE.md.Arun Isaac
2021-11-10Remove repeated input python-flask-cors.Arun Isaac
* guix.scm (genenetwork3)[propagated-inputs]: Remove python-flask-cors.
2021-11-10Indent guix.scm use-modules better.Arun Isaac
* guix.scm: Indent use-modules better, the more conventional way.
2021-11-10Set version to 0.1.0.Arun Isaac
Semantic versioning begins at 0.1.0, not 0.0.1. * guix.scm: Set genenetwork package version to 0.1.0.
2021-11-10Name source checkout in the store.Arun Isaac
* guix.scm: Name source checkout in the store to "genenetwork3-checkout".
2021-11-10Use git-predicate in guix.scm.Arun Isaac
* guix.scm: Do not import (srfi srfi-1), (srfi srfi-26), (ice-9 match), (ice-9 popen) and (ice-9 rdelim). Use git-predicate instead of git-file?. (git-file?): Delete function.
2021-11-09Add functions for updating groupsBonfaceKilz
2021-11-09Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
2021-11-09Implement remaining part of `partial_correlation_recursive` 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: implement remaining portion of `partial_correlation_recursive` function. * tests/unit/computations/test_partial_correlations.py: add parsing for new data format and update tests
2021-11-09Update test data: have both vectors and matricesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Delete the older test data that was only testing with `z` being a vector and replace it with data that has `z` being a vector or matrix from data item to data item.
2021-11-09Add new data processing utilityFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/data_helpers.py: New function (`partition_by`) * tests/unit/test_data_helpers.py: Tests for new function Add a function that approximates Clojure's `partition-by` function, to help with processing the data in a more functional way.
2021-11-09Fix bug: if three columns, ensure last is "z"Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Fix a bug, caught when the function is called in a recursive form, with the "z*" columns reducing for each cycle through the recursive form. As it was, the last cycle through the recursive form would end up with a DataFrame with the columns "x", "y", and "z0" rather than the columns "x", "y", "z". This commit handles that edge case to ensure that the column name is changed from "z0" to simply "z".
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.
2021-11-04Add pingouin as a dependencyFrederick Muriuki Muriithi
* The missing dependency is causing the check pipeline to fail.
2021-11-04Stub `determine_partials`Frederick Muriuki Muriithi
Issue: * Stub out `determine_partials` which is a migration of `web.webqtl.correlation.correlationFunction.determinePartialsByR` in GN1. The function in GN1 has R code from line 188 to line 344. This will need to be converted over to Python. This function will also need tests.
2021-11-04Implement `compute_partial_correlations_fast`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Implement `compute_partial_correlations_fast` that is a partial migration of `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsFast` in GN1. This function will probably be reworked once the dependencies are fully migrated. It also needs tests to be added.
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.
2021-11-04Fix some linting errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-04Parse single line from CSV fileFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/data_helpers.py: New function (parse_csv_line) * tests/unit/test_data_helpers.py: Add tests for new function (parse_csv_line) Add a function to parse a single line from a CSV file.
2021-11-04Add some condition checking functionsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add the `check_for_literature_info` and `check_symbol_for_tissue_correlation` functions to check for the presence of specific data.
2021-11-04Explicitly round the valuesFrederick Muriuki Muriithi
* Explicitly round the values to prevent issues with the type-checker
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 linting and typing errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-04Rework sorting: remove `compare_tissue_correlation_absolute_values`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * gn3/db/correlations.py: Remove the `compare_tissue_correlation_absolute_values` function which is no longer needed.
2021-11-04Complete `build_temporary_tissue_correlations_table`Frederick 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: Remove comments after updating usage of the function at call point * gn3/db/correlations.py: Complete the implementation of the `build_temporary_tissue_correlations_table` function
2021-11-04Complete implementation of `batch_computed_tissue_correlation`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Complete the implementation of the `batch_computed_tissue_correlation` function
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
2021-11-04Move `correlations_of_all_tissue_traits`Frederick 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 (`correlations_of_all_tissue_traits`). * gn3/db/correlations.py: delete function (`correlations_of_all_tissue_traits`). Move the function to `gn3.computations.partial_correlations` module and comment out the db-access code. Rework it to receive, as arguments, the data it previously fetched from the database, and add comments on future rework to get the function working again.
2021-11-04Add missing commaFrederick 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.
2021-11-04Move the function to computations moduleFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The function `batch_computed_tissue_correlation` is a pure computations function with no expressions accessing the database, as far as I can tell, therefore, this commit moves the function over to the gn3.computations.partial_correlations module that holds the pure computation functions.
2021-11-04Move the partial_correlations module to gn3.computationsFrederick Muriuki Muriithi
* Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Move the partial_correlations.py module to the gn3.computations module, since it contains the computations for partial correlations.
2021-11-04Remove if clauses: replace with dictFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Remove the if clauses to simplify the code flow: use a dictionary of queries and select the appropriate query from the dictionary instead.
2021-11-04Stub out `batch_computed_tissue_correlation` functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Stub out `batch_computed_tissue_correlation` function to be used in implementing the function down the line.
2021-11-04Complete `correlations_of_all_tissue_traits`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Complete the implementation of the `correlations_of_all_tissue_traits` function by providing a call to a non-implemented function.
2021-11-04Implement `fetch_gene_symbol_tissue_value_dict_for_trait`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Implement `fetch_gene_symbol_tissue_value_dict_for_trait` function which is a migration of the `web.webqtl.correlation.correlationFunction.getGeneSymbolTissueValueDictForTrait` function in GeneNetwork1.
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