| Age | Commit message (Expand) | Author |
|---|
| 2021-08-30 | Implement module for interfacing with rust-qtlreaper...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: move `generate_traits_file` function to new
module
* gn3/computations/qtlreaper.py: new module to interface with the
`rust-qtlreaper` utility.
* gn3/settings.py: Provide setting for the path to the `rust-qtlreaper`
utility
* qtlfilesexport.py: Move `random_string` function to new module. Update to
use functions in new module.
Provide a module with functions to be used to interface with
`rust-qtlreaper`. This module essentially contains all the functions that
are needed to build the files needed for, and to run the qtlreaper utility.
| Muriithi Frederick Muriuki |
| 2021-08-30 | Document acquired knowledge on `rust-qtlreaper`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: document format of the traits file
To assist future developers, and development of the system, this commit
documents some of the hard-won knowledge about the operation of the system
to ease future development of the system.
The documentation, if good, might also help with future onboarding of new
developers to the system.
| Muriithi Frederick Muriuki |
| 2021-08-28 | README: updated install instructions | Pjotr Prins |
| 2021-08-28 | Add explanation of using a guix profile | Pjotr Prins |
| 2021-08-28 | Fix issue that caused R/qtl to not use the first covariate when using stratif... | zsloan |
| 2021-08-27 | Test out generation of traits file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* As part of the development effort, this commit provides a proof-of-concept
as a reference for generating the traits data file.
It might be useful for verifying that the functions that are called are
working as is expected.
| Muriithi Frederick Muriuki |
| 2021-08-27 | Provide intermediate data in final results...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Seeing as not every requirement/feature has been migrated over at this time,
this commit just provides all the intermediate data representations in the
final return of the function for later use down the line.
| Muriithi Frederick Muriuki |
| 2021-08-27 | Export trait data to file...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide a function to export the given strains and traits data into a traits
file for use with `rust-qtlreaper`.
| Muriithi Frederick Muriuki |
| 2021-08-27 | Rework strains and trait values retrieval...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Rework the strains and values retrieval function to more closely correspond
to the working of the original code in GN1
| Muriithi Frederick Muriuki |
| 2021-08-26 | Added # permutations to verbose print | zsloan |
| 2021-08-26 | Update imported module name...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* guix.scm: (gn packages golang) ==> (gnu packages golang)
csvdiff has moved to upstream guix and been removed from latest
guix-bioinformatics.
| Muriithi Frederick Muriuki |
| 2021-08-26 | Add rust-qtlreaper...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* guix.scm: new dependency (rust-qtlreaper)
| Muriithi Frederick Muriuki |
| 2021-08-20 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_gener... | Muriithi Frederick Muriuki |
| 2021-08-20 | Fix typing issue(s) caught by mypy...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Use `Sequence` type not `Iterator` type
| Muriithi Frederick Muriuki |
| 2021-08-20 | Retrieve the strains with valid values...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.
| Muriithi Frederick Muriuki |
| 2021-08-20 | Add tests for ordering and implement function...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.
| Muriithi Frederick Muriuki |
| 2021-08-20 | Minor correlation fixes (#36)...* fix key error for (*tissue_cor) tissue correlation
* update tests for tissue correlation
* rename speed_compute to fast_compute
* pep8 formatting | Alexander Kabui |
| 2021-08-18 | Test the clustering...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.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Fix obvious linting errors...* Fix linting errors that do not change the function of the code.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Make child sequence a list...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Since the `slink` function assigns values to the `listcopy` variable and its
children, this commit ensures that the sequence is a list to allow for the
assignment.
If the child-sequence is a tuple, that would lead to an exception.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Provide top-level `riset` key-value pair...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the expected, top-level `riset` key-value pair and eliminate the
redundant key-value pair.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Add tests and fix errors caught with tests...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
| Muriithi Frederick Muriuki |
| 2021-08-18 | Fix errors: add in missing parenthesis...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Call the `cursor.fetchone()` function to get results. Without the
parenthesis, the code was trying to use the function itself as the results,
which was a bug, and would lead to failure.
| Muriithi Frederick Muriuki |
| 2021-08-18 | Initialise heatmap generation module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to
test out plotly features on the command-line.
* guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Test the clustering...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.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Fix obvious linting errors...* Fix linting errors that do not change the function of the code.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Make child sequence a list...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Since the `slink` function assigns values to the `listcopy` variable and its
children, this commit ensures that the sequence is a list to allow for the
assignment.
If the child-sequence is a tuple, that would lead to an exception.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Provide top-level `riset` key-value pair...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the expected, top-level `riset` key-value pair and eliminate the
redundant key-value pair.
| Muriithi Frederick Muriuki |
| 2021-08-17 | Add tests and fix errors caught with tests...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
| Muriithi Frederick Muriuki |
| 2021-08-17 | Fix errors: add in missing parenthesis...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Call the `cursor.fetchone()` function to get results. Without the
parenthesis, the code was trying to use the function itself as the results,
which was a bug, and would lead to failure.
| Muriithi Frederick Muriuki |
| 2021-08-16 | Merge branch 'main' into heatmap_generation | Muriithi Frederick Muriuki |
| 2021-08-16 | Merge pull request #32 from genenetwork/heatmap_decompose_db_retrieval...Heatmap decompose db retrieval | BonfaceKilz |
| 2021-08-12 | Initialise heatmap generation module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps/heatmaps.py: Initialise the module with some code to be used to
test out plotly features on the command-line.
* guix.scm: Add `python-plotly` and `python-pandas` as dependencies.
| Muriithi Frederick Muriuki |
| 2021-08-12 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix some errors caught by the linter.
| Muriithi Frederick Muriuki |
| 2021-08-12 | Import missing definitions...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Import some missing definitions.
| Muriithi Frederick Muriuki |
| 2021-08-11 | use normal function for correlation (#34)...* use normal function for correlation + rename functions
* update test for sample correlation
* use normal function for tissue correlation + rename functions | Alexander Kabui |
| 2021-08-09 | Build up the heatmap data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add code to compute and organise the data that will be used to draw the
final heatmap.
This varies significantly in how it works from the original, but it still
tries to retain the general flow of data.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Set up the trait dataset type correctly...* gn3/db/traits.py: setup `trait_dataset_type`
* tests/unit/db/test_traits.py: fix tests
The type ('Temp', 'Geno', 'Publish', and 'ProbeSet') relate to a trait's
dataset, and not the trait itself. This commit updates the code to take this
into consideration.
The dataset type is also set up from a trait's full name, therefore this
commit removes the `trait_type` argument from the `retrieve_trait_info`
function.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Retrieve the trait data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add functions to retrieve the `value`, `variance`, and `ndata` values for
any given trait.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Add missing arguments. Fix typo....Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix minor bugs in the code.
| Muriithi Frederick Muriuki |
| 2021-08-09 | Fix linting errors...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add module, class and function docstrings
* Deactivate some irrelevant pylint errors
* Fix indentations and line-lengths
| Muriithi Frederick Muriuki |
| 2021-08-08 | Update tests...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix tests to take current changes into consideration.
| Muriithi Frederick Muriuki |
| 2021-08-08 | Only load extra data if the traits have basic info...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Only load the extra trait data if the basic trait information is found.
| Muriithi Frederick Muriuki |
| 2021-08-08 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decom... | Muriithi Frederick Muriuki |
| 2021-08-07 | Add gunicorn support for production | Pjotr Prins |
| 2021-08-07 | Update info on running guix container | Pjotr Prins |
| 2021-08-05 | db: traits: Return unique values when fetching sample data | BonfaceKilz |
| 2021-08-05 | Merge branch 'main' of github.com:genenetwork/genenetwork3 into heatmap_decom... | Muriithi Frederick Muriuki |
| 2021-08-05 | Reorganise the database code...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Reorganise the code to separate the datasets from the traits, and to more
closely conform to the same flow as that in GN1
| Muriithi Frederick Muriuki |
| 2021-08-05 | Build up trait_name items from full name...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* The full name of the traits from search contains multiple parts to it, and
as such, we use it to retrieve the appropriate data and set it up in the
final trait_info dictionary that is produced.
| Muriithi Frederick Muriuki |
