Cell type annotation: Harmony/KNN workflow #836
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
dorien-er
changed the title
* cellranger mkgtf component working and tested * removed comments * changelog entry added * test unique attribute in result * multiple attribute par added * removed unused packages * use pytest, multiple attributes tested --------- Co-authored-by: DriesSchaumont <[email protected]>
Co-authored-by: Dries Schaumont <[email protected]>
* cellranger mkgtf component working and tested * removed comments * changelog entry added * test unique attribute in result * multiple attribute par added * removed unused packages * use pytest, multiple attributes tested --------- Co-authored-by: DriesSchaumont <[email protected]>
dorien-er
force-pushed
the
harmony-knn-annoation-workflow
branch
from
6bcfac3 to
e2049f1
Compare
dorien-er
changed the title
DriesSchaumont
requested changes
Dec 24, 2024
| - name: "--theta" | ||
| type: double | ||
| description: | | ||
| Diversity clustering penalty parameter. Specify for each variable in group.by.vars. |
There was a problem hiding this comment.
When reading this, I am not sure that I know what group.by.vars means here? Is it related to another argument?
| `distance` (weight points by the inverse of their distance) | ||
| - name: "--n_neighbors" | ||
| type: integer | ||
| default: 15 |
| roles: [ author, maintainer ] | ||
| - __merge__: /src/authors/weiwei_schultz.yaml | ||
| roles: [ contributor ] | ||
|
|
There was a problem hiding this comment.
Could you add the test_dependencies to info?
Comment on lines
+9
to
+12
| | map {id, state -> | ||
| def new_state = state + ["workflow_output": state.output] | ||
| [id, new_state] | ||
| } |
There was a problem hiding this comment.
Suggested change
| | map {id, state -> | |
| def new_state = state + ["workflow_output": state.output] | |
| [id, new_state] | |
| } | |
| | map {id, state -> | |
| def new_state = state + ["workflow_output": state.output] | |
| [id, new_state] | |
| } |
Comment on lines
+13
to
+17
| // add id as _meta join id to be able to merge with source channel and end of workflow | ||
| | map{ id, state -> | ||
| def new_state = state + ["_meta": ["join_id": id]] | ||
| [id, new_state] | ||
| } |
There was a problem hiding this comment.
Is _meta required here? I think the number of input and output events from this workflow are the same and that the IDs of the events match?
| } | ||
| | view {"After adding join_id: $it"} | ||
| // Add 'query' id to .obs columns of query dataset | ||
| | add_id.run( |
There was a problem hiding this comment.
add_id and duplicate_obs could be performed in parallel here by:
- splitting the input channel into two channels: one for the reference and one for the query
- performing
add_idandduplicate_obs - joining the channel back together
And since you have add_id and duplicate_obstwice, please add a key argument to .run (e.g. key: "add_id_query" and key: "add_id_reference" ). This makes sure that the process names remain unique.
|
|
||
| assert "rna" in list(input_mudata.mod.keys()), "Input should contain rna modality." | ||
| assert all(key in list(input_mudata.mod["rna"].obsm) for key in expected_obsm), f"Input mod['rna'] obs columns should be: {expected_obsm}, found: {input_mudata.mod['rna'].obsm.keys()}." | ||
| assert all(key in list(input_mudata.mod["rna"].obs) for key in expected_obs), f"Input mod['rna'] obs columns should be: {expected_obs}, found: {input_mudata.mod['rna'].obs.keys()}." |
There was a problem hiding this comment.
Would it be possible to add the contents of the newly created columns? (for example that the predictions are in fact labels and the probabilities are floats?)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Changelog
Workflow for harmony integration followed by KNN label transfer for cell type annotation.
Issue ticket number and link
Closes #xxxx (Replace xxxx with the GitHub issue number)
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributor's guide
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI tests succeed!