| Age | Commit message (Expand) | Author |
|---|
| 2023-10-06 | Pass in configs/settings as function arguments...To avoid reliance of `flask.current_app.config` or on `gn3.settings` modules
globally, this commit passes in the appropriate configurations as arguments to
the relevant functions.
| Frederick Muriuki Muriithi |
| 2022-12-21 | gn3: (gn3.random -> gn3.chancy): Rename module to avoid conflicts....Rename the `gn3.random` module to gn3.chancy to avoid conflicts with Python's
`random` module.
* gn3/random.py -> gn3/chancy.py: rename module
* gn3/commands.py: update import
* gn3/computations/partial_correlations.py: update import
* gn3/computations/qtlreaper.py: update import
* gn3/computations/rust_correlation.py: update import
* gn3/db/correlations.py: update import
* gn3/db/traits.py: update import
* gn3/heatmaps.py: update import
* tests/integration/conftest.py: update import
| Frederick Muriuki Muriithi |
| 2022-02-21 | Fix a myriad of linter issues...* 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
| Frederick Muriuki Muriithi |
| 2021-11-11 | Remove redundant check on the Pearson correlation coefficient....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.
| Arun Isaac |
| 2021-10-19 | Move 'export_trait_data' to 'gn3.db.traits' module...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* gn3/db/traits.py: Move function `export_trait_data` here
* gn3/heatmaps.py: Remove function `export_trait_data`
* tests/unit/db/test_traits.py: Move function `export_trait_data` tests here
* tests/unit/test_heatmaps.py: Remove function `export_trait_data` here
Function `export_trait_data` more closely corresponds to the traits and is
used in more than just the `gn3.heatmaps` module. This commit moves the
relevant code over to the `gn3.db.traits` module and also moves the tests to
the corresponding tests modules.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Fix some linting issues | Frederick Muriuki Muriithi |
| 2021-10-19 | Enable vertical orientation of heatmaps...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Update the code to enable the generation of the heatmap in both the
horizontal and vertical orientations.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Swap axis labels...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Switch the axis labels to make them less confusing for the user.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Add typing. Simplify arguments....Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Add type-hints to the functions
* Merge the axis data and labels to simpler dict arguments to reduce number of
parameters to the function.
| Frederick Muriuki Muriithi |
| 2021-10-19 | Remove file I/O statements...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/non-clustered-heatmaps-and-flipping.gmi
* Remove file I/O from the function. If file I/O is needed, it will be
provided outside of this function.
| Frederick Muriuki Muriithi |
| 2021-09-28 | Provide loci names to heatmap...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the loci names to the heatmaps so that hovering over the heatmap
cells displays the associated locus name.
| Frederick Muriuki Muriithi |
| 2021-09-28 | Retrieve loci names ordered by chromosomes...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps.py: implement function
* tests/unit/test_heatmaps.py: add test
Add a function to retrieve the loci names from the traits, ordered by
chromosomes, in alphabetical order.
This is useful to provide the user with more information on hovering over
the heatmap cells: each cell will now display the locus name, trait name and
value associated with it.
| Frederick Muriuki Muriithi |
| 2021-09-28 | Approximate single-spectrum colour scale in GN1...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* To provide a somewhat similar experience to GeneNetwork1, this commit
approximates the single-spectrum colour scale in GeneNetwork1 for the
heatmaps in GeneNetwork3.
Work to get the multiple-spectrum colour sc(ales/hemes) will be done in
other commits, since that might require digging even deeper into Plotly's
guts to figure out.
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `riset` to `group`...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update terminology to use the appropriate domain terminology according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926041744
| Frederick Muriuki Muriithi |
| 2021-09-27 | Update terminology: `strain` to `sample`...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
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix typing issues...* Ignore some errors
* Update typing definitions for some portions of code
* Add missing imports
| Frederick Muriuki Muriithi |
| 2021-09-22 | Fix pylint errors...* Add missing function and module docstrings
* Remove unused imports
* Fix import order
* Rework some code sections to fix issues
* Disable some pylint errors.
| Frederick Muriuki Muriithi |
| 2021-09-22 | Return serialized plotly figure...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Serialize the figure to JSON
* gn3/heatmaps.py: Return the figure object
Serialize the Plotly figure into JSON, and return that, so that it can be
used on the client to display the image.
| Frederick Muriuki Muriithi |
| 2021-09-20 | Return only the data...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/api/heatmaps.py: Parse incoming data to build up correct trait names and
respond with only the computed heatmap data.
* gn3/heatmaps.py: Return only the computed data for heatmaps and clustering.
Since GN3 is supposed to handle only the data, and db-access, this commit
ensures that GN3 responds to the client with only the computed heatmap data,
and does not try to generate the heatmaps themselves.
The generation of the heatmaps will be delegated to the UI clients, such as
GeneNetwork2.
| Frederick Muriuki Muriithi |
| 2021-09-17 | Fix a number of linting issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Frederick Muriuki Muriithi |
| 2021-09-17 | Fix some layout issues and update colorscale...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the plot layouts and size to display the dendrogram and individual
chromosome heatmaps side by side
* Update the colour scale to begin with the grays rather than absolute black
| Frederick Muriuki Muriithi |
| 2021-09-17 | Create dendrogram to show clustering tree...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Provide the clustering data to be used for the creation of the clustering
dendrogram in the final clustered heatmap plot.
| Frederick Muriuki Muriithi |
| 2021-09-16 | Fix minor bugs...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix a few minor bugs left over from the integration of code from the
proof-of-concept code.
| Frederick Muriuki Muriithi |
| 2021-09-16 | Add missing imports...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add missing imports that are needed in the code.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Update entry-point function for heatmap generation...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Copy over code from the proof-of-concept implementation and clean it up a
little for the entry-point function for heatmap generation via the API
| Frederick Muriuki Muriithi |
| 2021-09-15 | Generate heatmaps in a single plot...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Add a function to generate the heatmaps for each chromosome into a single
plot.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Process data into format usable by heatmaps...* gn3/heatmaps.py: implement `process_traits_data_for_heatmap` function, that
will process the data into a form usable by heatmaps.
* tests/unit/test_heatmaps.py: check that the function processes the data into
the correct form.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Integrate get_lsr_from_chr function...* gn3/heatmaps.py: copy over function
* tests/unit/test_heatmaps.py: add tests
Copy function over from proof of concept and add some tests to ensure it
works as expected.
| Frederick Muriuki Muriithi |
| 2021-09-15 | Reorganise modules...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.
| Frederick Muriuki Muriithi |
