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The `fix_strains` function works on the trait data, not the basic trait
info. This commit fixes the arguments passed to the function, and also some
bugs in the function.
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* compute zscore function
* test case for computing zscore
* function to compute pca
* generate scree plot data
* generate new pca trait data from zscores and eigen_vec
* remove redundant functions
* generate factor loading table data
* generate pca temp dataset dict
* variable naming and error fixes
* unit test for processing factor loadings
* minor fixes for generating temp pca dataset
* pass datetime as argument to generate_pca temp dataset function
* add unittest for caching pca datasets
* cache temp datasets
* ignore missing imports for sklearn
* mypy fixes
* pylint fixes
* refactor tests for pca
* remove ununsed imports
* fix for generating pca traits vals
* mypy and code refactoring
* pep8 formatting and add docstrings
* remove comments /pep8 formatting
* sort eigen vectors based on eigen values
* minor fix for zscores
* fix for rounding variance ratios
* refactor tests
* rename module to pca
* rename datasets to traits
* fix failing tests
* fix caching function
* fixes return x and y coordinates for scree plot
* expand exception scope
* fix for deprecated numpy.matrix function
* fix for failing tests
* pep8 fixes
* remove comments
* fix merge conflict
* pylint fixes
* rename module name to test_pca
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When the encoding is not specified explicitly, the system default encoding is
used. This is not recommended.
* gn3/computations/ctl.py (call_ctl_script),
gn3/computations/gemma.py (generate_pheno_txt_file),
gn3/computations/parsers.py (parse_genofile),
gn3/computations/partial_correlations.py (partial_correlations_fast),
gn3/computations/rqtl.py (process_rqtl_output, process_perm_output),
gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script),
gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file
encoding.
*
tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file),
tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test
for call to open with encoding='utf-8' argument.
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* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
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Use pytest's `mark` feature to explicitly categorise the tests and run them
per category
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Add property tests using pytest and hypothesis to test that the expected
properties hold for the
`gn3.computations.partial_correlations.dictify_by_samples`
function.
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Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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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.
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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
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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.
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* 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.
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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.
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partial-correlations
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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.
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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.
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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.
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partial-correlations
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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
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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.
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Fix these later. I need a passing test suite so as to update the gn2 docker
image.
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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
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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.
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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.
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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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/computations/partial_correlations.py: Implement one path for the
`gn3.computations.partial_correlations.partial_correlation_recursive`
function.
* gn3/settings.py: Add a setting for how many decimal places to round to
* tests/unit/computations/test_partial_correlations.py: Update test to take
the number of decimal places into consideration
Implement a single path (where the z value is a vector and not a matrix) for
the `partial_correlation_recursive` function.
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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 (`build_data_frame`)
* tests/unit/computations/test_partial_correlations.py: Add tests for new
function
Add a new function to build a pandas DataFrame object from the provided
values:
- x: a vector of floats (represented with a tuple of floats)
- y: a vector of floats (represented with a tuple of floats)
- z: a vector OR matrix of floats (represented with a tuple of floats or a
tuple of tuples of floats)
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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.
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partial-correlations
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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.
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* 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
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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.
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Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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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.
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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
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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.
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