genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2021-09-27	Update terminology: `riset` to `group`	Frederick Muriuki Muriithi
	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
2021-09-27	Update terminology: `strain` to `sample`	Frederick Muriuki Muriithi
	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
2021-09-22	Fix typing issues	Frederick Muriuki Muriithi
	* Ignore some errors * Update typing definitions for some portions of code * Add missing imports
2021-09-22	Fix pylint errors	Frederick Muriuki Muriithi
	* Add missing function and module docstrings * Remove unused imports * Fix import order * Rework some code sections to fix issues * Disable some pylint errors.
2021-09-22	Return serialized plotly figure	Frederick Muriuki Muriithi
	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.
2021-09-20	Return only the data	Frederick Muriuki Muriithi
	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.
2021-09-17	Fix a number of linting issues	Frederick Muriuki Muriithi
	Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-09-17	Fix some layout issues and update colorscale	Frederick Muriuki Muriithi
	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
2021-09-17	Create dendrogram to show clustering tree	Frederick Muriuki Muriithi
	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.
2021-09-16	Fix minor bugs	Frederick Muriuki Muriithi
	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.
2021-09-16	Add missing imports	Frederick Muriuki Muriithi
	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.
2021-09-15	Update entry-point function for heatmap generation	Frederick Muriuki Muriithi
	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
2021-09-15	Generate heatmaps in a single plot	Frederick Muriuki Muriithi
	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.
2021-09-15	Process data into format usable by heatmaps	Frederick Muriuki Muriithi
	* 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.
2021-09-15	Integrate get_lsr_from_chr function	Frederick Muriuki Muriithi
	* 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.
2021-09-15	Reorganise modules	Frederick Muriuki Muriithi
	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.