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path: root/gn3/heatmaps.py
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2021-10-19Move '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
2021-10-19Fix some linting issuesFrederick Muriuki Muriithi
2021-10-19Enable 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
2021-10-19Swap 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
2021-10-19Add 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
2021-10-19Remove 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
2021-09-28Provide 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
2021-09-28Retrieve 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
2021-09-28Approximate 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
2021-09-27Update 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
2021-09-27Update 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
2021-09-22Fix typing issues...* Ignore some errors * Update typing definitions for some portions of code * Add missing imports Frederick Muriuki Muriithi
2021-09-22Fix 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
2021-09-22Return 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
2021-09-20Return 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
2021-09-17Fix 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
2021-09-17Fix 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
2021-09-17Create 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
2021-09-16Fix 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
2021-09-16Add 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
2021-09-15Update 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
2021-09-15Generate 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
2021-09-15Process 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
2021-09-15Integrate 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
2021-09-15Reorganise 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