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2022-01-27Refactor: Remove circular importrefactor-circular-importFrederick Muriuki Muriithi
The function `gn3.computation.partial_correlations.correlations_of_all_tissue_traits` was, before this commit, called inside the `gn3.db.correlations.build_temporary_tissue_correlations_table` function, leading to a circular dependency. This commit removes the circular dependency by rearranging the calls.
2022-01-22process ctl plot data imgAlexander Kabui
2022-01-22read stdout data;handle exceptionsAlexander Kabui
2022-01-22init file to call ctl scriptAlexander Kabui
2022-01-12Update return type. Remove duplicate import.Frederick Muriuki Muriithi
The function is a generator function, since it uses a `yield` statement, and thus returns a generator object, that contains a tuple object. This fixes that. We also remove a duplicate import.
2022-01-10Use the correct letter case for the keysFrederick Muriuki Muriithi
* Use the correct case for the keys inorder to retrieve the correct values.
2022-01-10Indicate that string is an f-stringFrederick Muriuki Muriithi
* The string had the f-string syntax to format the values to be inserted into the string, but was missing the 'f' before the opening quotes to signify to python that this was an f-string. This commit fixes that.
2022-01-10Remove all pairs with 'None' as the valueFrederick Muriuki Muriithi
* Remove all key-value pairs whose value is None.
2022-01-10Replace unoptimised function with optimised oneFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace unoptimised function with one optimised to give better performance. The optimisation done here is to fetch multiple items/traits from the database per query, rather than the original form, which fetched a single item/trait from the database per query.
2022-01-10Convert NaN to NoneFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi Comment: https://github.com/genenetwork/genenetwork3/pull/67#issuecomment-1000828159 * Convert NaN values to None to avoid possible bugs with the string replace method used before.
2022-01-10Add optimised entry for partial correlationsFrederick Muriuki Muriithi
Issue: * Function `gn3.computations.partial_correlations_optimised.partial_correlations_entry` is a copy of the `gn3.computations.partial_correlation.partial_correlations_entry` function that is optimised for better performance. The optimised function is intended to replace the unoptimised one, but it is included in this commit for comparison purposes, and to maintain some historical context for doing it this way.
2022-01-10Rework database functions to fetch multiple itemsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * In an attempt to optimise the performance of the partial correlations feature, this commit reworks some database access functions to fetch multiple items from the database, per query, unlike their original forms which would fetch a single item per query. This reduces queries to the database, and should hopefully improve the responsiveness of the partial correlations feature.
2022-01-05Merge pull request #64 from jgarte/type-hint-normalize-valuesBonfaceKilz
Adds type hint for normalize_values function
2021-12-24Fix typing errorsFrederick Muriuki Muriithi
2021-12-24Fix linting errorsFrederick Muriuki Muriithi
2021-12-24Fix sortingFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Update the sorting algorithm, for literature and tissue correlations so that it sorts the results by the correlation value first then by the p-value next.
2021-12-24Return the correlation method usedFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Return the correlation method used
2021-12-24Reduce the total amount of data to be outputFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * There is a lot of data that is not necessary in the final result. This commit removes that data, retaining only data relevant for the display.
2021-12-24Add dataset type to the resultsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * The dataset type is relevant for the display of the data, therefore, this commit presents the dataset type as part of the results.
2021-12-17Add "success" status to final computation resultsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-12-14linting: Fix obvious linting issuesFrederick Muriuki Muriithi
2021-12-14mypy: ignore some imports and errorsFrederick Muriuki Muriithi
* Ignore some missing library stubs * Ignore some typing errors * Fix obvious typing errors
2021-12-14Adds type hint for normalize_values functionjgart
2021-12-14TO REVERT: Add logging to see data frameFrederick Muriuki Muriithi
2021-12-14Remove any items with less than 3 samplesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * pingouin raises an exception whenever one attempts to use it to compute the partial correlation with data that has less than 3 samples.
2021-12-14Fix dataset: use target dataset not primaryFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Use the target dataset to load the target traits, not the primary trait's dataset, since they might differ.
2021-12-13Provide missing functionFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Import the missing function.
2021-12-13Fix the removal of controls for corresponding Nones in targetsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Fix the code, so that it removes all control values, whose corresponding target values are None, without throwing an error.
2021-12-13Return the primary and control traits in addition to resultsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * In addition to the partial correlation results, this commit enables the return of the chosen primary trait and the selected control traits. This data is required for presentation on the results page.
2021-12-13Run partial correlations against chosen databaseFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Run the partial correlations against the database that the user selects, and not the one from which the primary trait is. This was a bug in the code.
2021-12-10format normalize function doc stringAlexander Kabui
2021-12-10minor pr fixesAlexander Kabui
2021-12-10rename variablesAlexander Kabui
2021-12-10try and catch for non matching sample keysAlexander Kabui
2021-12-10update function docs for normalizing strain valuesAlexander Kabui
2021-12-10fix bug:unpacking error when generator returns empty listAlexander Kabui
2021-12-09Prevent error on no result. Fix indexingFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * If the dataset name is not found, don't cause an exception, instead, return the provided search name. * Use the correct inner object
2021-12-08Provide group from primary traitFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * From the collections page, the group is not present, so this commit retrieves the group value from the primary trait.
2021-11-29Fix linting errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
2021-11-29Provide entry-point function for the partial correlationsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Provide the entry-point function to the partial correlation feature. This is the function that ochestrates the fetching of the data, and processing it for output by the API endpoint (to be implemented).
2021-11-23Fix a myriad of linting errorsFrederick Muriuki Muriithi
* Fix linting errors like: - Unused variables - Undeclared variable errors (mostly caused by typos, and wrong names) - Missing documentation strings for functions etc.
2021-11-23Migrate `getPartialCorrelationsNormal`Frederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Migrate the `web.webqtl.correlation.PartialCorrDBPage.getPartialCorrelationsNormal` function in GN1. * Remove function obsoleted by newer implementation of the code
2021-11-19Avoid rounding: compare floats approximatelyFrederick Muriuki Muriithi
Notes: https://github.com/genenetwork/genenetwork3/pull/56#issuecomment-973798918 * As mentioned in the notes, rather than rounding to an arbitrary number of decimal places, it is a much better practice to use approximate comparisons of floats for the tests.
2021-11-18Fix some linting errorsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Fix some obvious linting errors and remove obsolete code
2021-11-18Replace code migrated from R with pingouin functionsFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Replace the code that was in the process of being migrated from R in GeneNetwork1 with calls to pingouin functions that achieve the same thing. Since the functions in this case are computing correlations and partial correlations, rather than having home-rolled functions to do that, this commit makes use of the tried and tested pingouin functions. This avoids complicating our code with edge-case checks, and leverages the performance optimisations done in pingouin.
2021-11-15Fix bugs in recursive partial correlationsFrederick Muriuki Muriithi
* gn3/computations/partial_correlations.py: Remove rounding. Fix computation of remaining covariates * tests/unit/computations/partial_correlations_test_data/pcor_rec_blackbox_test.txt: reduce the number of covariates to between one (1) and three (3) * tests/unit/computations/test_partial_correlations.py: fix some minor bugs It turns out that the computation complexity increases exponentially, with the number of covariates. Therefore, to get a somewhat sensible test time, while retaining a large-ish number of tests, this commit reduces the number of covariates to between 1 and 3.
2021-11-15Fix the columns in built data frameFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * When the z value is a Sequence of sequences of values, each of the internal sequences should form a column of its own, and not a row, as it was originally set up to do.
2021-11-12Merge branch 'main' of github.com:genenetwork/genenetwork3 into ↵Frederick Muriuki Muriithi
partial-correlations
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.
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