AllenInstitute / AllenInstitute/cell_type_mapper
Clarify number of bootstrapping iterations for web tool
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- Dominant language
- Python
- Stars
- 55
- Forks
- 9
- PR merge metrics
- No merged PRs in 30d
Description
Hello, from the explanation
Recall that hierarchical mapping maps the cell 100 times, using a random subset of marker genes for each iteration, and assigning the cell to the cell type that is most correlated with the cell in the plurality of those 100 iterations. bootstrapping_probability is the fraction of the 100 iterations that chose the final assignment"
in this example I was able to infer that the number of bootstrap iterations used for the web portal is 100 and then confirmed this by finding the section at the bottom of the downloaded output .json that notes the config and type assignment values.
Could the default bootstrap iterations be noted on the web portal page to make that key value clearer to users? Additionally, could the config section of the results be moved to a separate file to make them easier to find/review for users who might not be familiar with the format or expect those values to be reported in that file along with the per cell outputs? I understand that the code base is used for both the command line and web portal options and the command line option makes the config values very clear since they are defined upfront by the user but for documentation/reproducibility of the web version it would be helpful to have those values reported in a way that's easier to find.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the linked explore_mapping_results.ipynb example and inspect the downloaded output JSON, especially its bottom config and type-assignment section. Then trace how the web portal presents the bootstrap setting and serializes results. Done means the default of 100 iterations is clearly shown in the web portal and configuration values are easier to find or review.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- documentation, web-dev
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100