n_components parameter for t-SNE
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Description
- Additional function parameters / changed functionality / changed defaults?
Could you please add n_components parameter for tSNE embedding? sklearn t-SNE implementation allows to set this parameter. At the moment even setting n_pcs to 3 and use_rep to three-dimensional X_pca produces two-dimensional output.
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
Locate Scanpy's t-SNE entry point and compare its available parameters with scikit-learn's t-SNE implementation. Trace how n_pcs and use_rep determine the embedding shape, then add support for selecting n_components and verify that a three-dimensional input can produce three-dimensional output.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, scikit-learn
- Domain
- data-visualization, machine-learning
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100