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2021-09-22init endpoint tests for wgcnaAlexander Kabui
2021-09-20Enable Cross-Origin Resource SharingFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/api/heatmaps.py: Fix bugs in data parsing * gn3/app.py: enable CORS * gn3/settings.py: add flask-cors configurations * guix.scm: Add flask-cors dependency For easier testing of the heatmaps generation feature, this commit activates the cross-origin resource sharing for all "localhost" origins.
2021-09-20Remove proof-of-concept test codeFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Remove the proof-of-concept CLI-only module that was used to learn how the heatmaps work and identify the appropriate data for use with them.
2021-09-20Return only the dataFrederick 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.
2021-09-17Fix a number of linting issuesFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
2021-09-17Return path to generated filename for nowFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * To help with demonstrating that the code is producing the expected output, for now, we return the path to the generated html file that displays the interactive heatmap. At this point, it is mostly useful in the development environment. Moving forward, we might have to actually stream the raw html, or if we can get the Kaleido library packaged for GNU Guix, stream the images binary data instead.
2021-09-17Fix some layout issues and update colorscaleFrederick 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
2021-09-17Create dendrogram to show clustering treeFrederick 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.
2021-09-16pylint fixesAlexander Kabui
2021-09-16Add WGCNA_SCRIT env to settingsAlexander Kabui
2021-09-16init tests for wgcnaAlexander Kabui
2021-09-16pass user input to call scriptAlexander Kabui
2021-09-16Intergrate the heatmap generation with the APIFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Intergrate the heatmap generation code on the /api/heatmaps/clustered endpoint. The endpoint should take a json query of the form: {"traits_names": [ ... ] } where the "traits_name" value is a list of the full names of traits. A sample query to the endpoint could be something like the following: curl -i -X POST "http://localhost:8080/api/heatmaps/clustered" \ -H "Accept: application/json" \ -H "Content-Type: application/json" \ -d '{ "traits_names": [ "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672", "UCLA_BXDBXH_CARTILAGE_V2::ILM2260338", "UCLA_BXDBXH_CARTILAGE_V2::ILM3140576", "UCLA_BXDBXH_CARTILAGE_V2::ILM5670577", "UCLA_BXDBXH_CARTILAGE_V2::ILM2070121", "UCLA_BXDBXH_CARTILAGE_V2::ILM103990541", "UCLA_BXDBXH_CARTILAGE_V2::ILM1190722", "UCLA_BXDBXH_CARTILAGE_V2::ILM6590722", "UCLA_BXDBXH_CARTILAGE_V2::ILM4200064", "UCLA_BXDBXH_CARTILAGE_V2::ILM3140463" ] }' which should respond with a json response containing the raw binary string for the png format and possibly another for the svg format.
2021-09-16Fix minor bugsFrederick 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.
2021-09-16Add missing importsFrederick 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.
2021-09-16run cmd and add exception handlerAlexander Kabui
2021-09-16register wgcna blueprintAlexander Kabui
2021-09-16add initial endpoint for wgcnaAlexander Kabui
2021-09-16add function to compose and run wgcna scriptAlexander Kabui
2021-09-16function to parse form data and write to json fileAlexander Kabui
2021-09-15initial test file for wgcnaAlexander Kabui
2021-09-15init wgcna file to run r script and preprocess dataAlexander Kabui
2021-09-15remove golang package causing build failureAlexander Kabui
2021-09-15Update entry-point function for heatmap generationFrederick 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
2021-09-15Generate heatmaps in a single plotFrederick 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.
2021-09-15Process data into format usable by heatmapsFrederick 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.
2021-09-15Integrate get_lsr_from_chr functionFrederick 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.
2021-09-15Reorganise modulesFrederick 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.
2021-09-15Fix format of arguments and expected valuesFrederick Muriuki Muriithi
* tests/unit/computations/test_heatmap.py: ordering is not longer provided as a list of tuples; the ordering values are just a list of numbers now. This commit updates the test to take this into consideration. * tests/unit/computations/test_qtlreaper.py: the 'Chr' value if numeric, is represented by an actual number, not a string. This commit updates the code to take this into consideration.
2021-09-15Add missing sample file for testsFrederick Muriuki Muriithi
* tests/unit/db/data/genotypes/genotype_sample1.geno: new file Add a missing sample data file needed for unit tests.
2021-09-15minor fixesAlexander Kabui
2021-09-15rename variables && delete debugsAlexander Kabui
2021-09-15Fetch IMAGE_DIR env and add img locationAlexander Kabui
2021-09-14remove debug statementsAlexander Kabui
2021-09-14function to generate rand str for imageAlexander Kabui
2021-09-14plot plotDendroAndColors and generate pngAlexander Kabui
2021-09-14construct gene co-expression network & module detectionAlexander Kabui
2021-09-14compute the softthreshholdAlexander Kabui
2021-09-14Checking data for excessive missing valuesAlexander Kabui
2021-09-14load the required data for analysisAlexander Kabui
2021-09-14init commit for wgcna scriptAlexander Kabui
2021-09-09Update proof-of-concept codeMuriithi Frederick Muriuki
* Add individual heatmaps * Add dendograms * Merge multiple heatmaps to single plot Updated the proof of concept code to provide a sample of what is needed to generate the appropriate heatmaps. To generate the sample heatmaps, one can run something like: env SQL_URI="mysql://webqtlout:webqtlout@127.0.0.1:3306/db_webqtl" \ python3 qtlfilesexport.py assuming that the database can be accessed at 127.0.0.1:3306
2021-09-08Ease search for traits and chromosomesMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Return a dict of values rather than list for the traits and chromosomes to ease searching through the data.
2021-09-08Parse Chr value as int where possibleMuriithi Frederick Muriuki
* To ease sorting of data by numerical order down the line, sort the "Chr" values by numerical order.
2021-09-08Remove extraneous text to ease sortingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Change the id from 'T<n>' to simply '<n>' to ease sorting of the trait results by numerical order rather than string order.
2021-09-08Fix the traits order computations for clusteringMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * gn3/computations/heatmap.py: Fix ordering function * tests/unit/computations/test_heatmap.py: update test The order of the traits is important for the clustering algorithm, since the clustering seems to use the distance of one trait from another to determine how to order them. This commit also gets rid of the xoffset argument that is not important to the ordering, and was used in the older GN1 to determine how to draw the clustering lines.
2021-09-06Provide function to organise parsed QTLReaper resultsMuriithi Frederick Muriuki
* gn3/computations/qtlreaper.py: Provide a function to organise the results by trait for easier use down the line. * tests/unit/computations/test_qtlreaper.py: provide a test to ensure that the organising function works as expected.
2021-09-06Leave "Chr" value as string when parsingMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * The "Chr" value seems to be mostly a name of some sort, despite it being, seemingly an number. This commit parses the "Chr" value as a string. It also updates the tests to expec a string, rather than a number for "Chr" values.
2021-09-06Handle type-coercion exceptionsMuriithi Frederick Muriuki
* gn3/computations/qtlreaper.py: handle exceptions Sometimes, the values being parsed are plain strings and cannot be cast to the float types. This commit handles that by casting only those values that can be cast to float, and returning the others as strings.
2021-09-06Find nearest markerMuriithi Frederick Muriuki
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Migrate the `web.webqtl.heatmap.Heatmap.getNearestMarker` function in GN1 to GN3.
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