| Age | Commit message (Expand) | Author |
|---|
| 2021-09-27 | fix merge conflicts | Alexander Kabui |
| 2021-09-27 | Remove unnecessary variable....Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Fix issue according to review
https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714549781
| Frederick Muriuki Muriithi |
| 2021-09-27 | Narrow the exception and add comments...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Only catch the `FileExistsError` allowing any other exception to pass
through. This tries to conform a little to the review at
https://github.com/genenetwork/genenetwork3/pull/37#discussion_r714552696
| 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 |
| 2021-09-23 | minor fixes for endpoint | Alexander Kabui |
| 2021-09-23 | Return r error if returncode!=0 | Alexander Kabui |
| 2021-09-23 | read generated files from r and return output | Alexander Kabui |
| 2021-09-22 | Fix more pylint errors | 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 | Update check: Heatmaps need at least 2 items...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the check to look for at least 2 traits before trying to generate the
heatmap.
| 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 |
| 2021-09-22 | jsonify results | Alexander Kabui |
| 2021-09-20 | Enable Cross-Origin Resource Sharing...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.
| 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 | Return path to generated filename for now...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.
| 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 | Add WGCNA_SCRIT env to settings | Alexander Kabui |
| 2021-09-16 | pass user input to call script | Alexander Kabui |
| 2021-09-16 | Intergrate the heatmap generation with the API...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.
| 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 |
| 2021-09-16 | run cmd and add exception handler | Alexander Kabui |
| 2021-09-16 | register wgcna blueprint | Alexander Kabui |
| 2021-09-16 | add initial endpoint for wgcna | Alexander Kabui |
| 2021-09-16 | add function to compose and run wgcna script | Alexander Kabui |
| 2021-09-16 | function to parse form data and write to json file | Alexander Kabui |
| 2021-09-15 | init wgcna file to run r script and preprocess data | Alexander Kabui |
| 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 |
| 2021-09-08 | Ease search for traits and chromosomes...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.
| Muriithi Frederick Muriuki |
| 2021-09-08 | Parse Chr value as int where possible...* To ease sorting of data by numerical order down the line, sort the "Chr"
values by numerical order.
| Muriithi Frederick Muriuki |
| 2021-09-08 | Remove extraneous text to ease sorting...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.
| Muriithi Frederick Muriuki |
| 2021-09-08 | Fix the traits order computations for clustering...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.
| Muriithi Frederick Muriuki |
| 2021-09-06 | Provide function to organise parsed QTLReaper results...* 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.
| Muriithi Frederick Muriuki |
| 2021-09-06 | Leave "Chr" value as string when parsing...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.
| Muriithi Frederick Muriuki |
| 2021-09-06 | Handle type-coercion exceptions...* 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.
| Muriithi Frederick Muriuki |
| 2021-09-06 | Find nearest marker...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.
| Muriithi Frederick Muriuki |
| 2021-09-03 | Add covarstruct as a possible keyword for the rqtl_wrapper.R script (not inte... | zsloan |
| 2021-09-01 | Fix linting and typing issues...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
| Muriithi Frederick Muriuki |
| 2021-09-01 | Built top-level genotype file parsing function...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype files
* tests/unit/db/test_genotypes.py: test parsing is correct
Add the overall genotype files parsing function and tests to check that the
parsing works as expected.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse data lines into markers...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse data lines in file to genetic markers.
* tests/unit/db/test_genotypes.py: test that parsing works.
Add some tests to check that the parsing of the markers works as expected,
and add the code to actually parse the markers.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Parse the genotype file's data header...* gn3/db/genotypes.py: parse data header
* tests/unit/db/test_genotypes.py: check that header's parse works correctly.
Add tests to check that the parser works as expected. Add code to implement
the parsing and pass the tests.
| Muriithi Frederick Muriuki |
| 2021-09-01 | Implement parsing of genotype labels...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/db/genotypes.py: parse genotype labels
* tests/unit/db/test_genotypes.py: test that genotype labels are parsed
correctly
As part of parsing the genotype files into usable python data structures,
this commit adds a function to parse the label lines (beginning with "@")
into the appropriate values.
| Muriithi Frederick Muriuki |
