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(feat): add n_components parameter to tSNE - #2803

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flying-sheep merged 7 commits into
scverse:mainfrom
ch1ru:master
May 15, 2025
Merged

(feat): add n_components parameter to tSNE#2803
flying-sheep merged 7 commits into
scverse:mainfrom
ch1ru:master

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@ch1ru

@ch1ru ch1ru commented Jan 11, 2024

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Added the n_components parameter in the tsne function, similar to the one in umap and updated docstring.

  • Release notes not necessary because: Only minor change.

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codecov Bot commented Jan 11, 2024

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 72.84%. Comparing base (c410cd1) to head (88d721c).
Report is 76 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #2803   +/-   ##
=======================================
  Coverage   72.84%   72.84%           
=======================================
  Files         111      111           
  Lines       12368    12368           
=======================================
  Hits         9009     9009           
  Misses       3359     3359           
Files Coverage Δ
scanpy/tools/_tsne.py 90.69% <ø> (ø)

@flying-sheep flying-sheep added this to the 1.12.0 milestone May 8, 2025
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Thanks!

@flying-sheep
flying-sheep enabled auto-merge (squash) May 8, 2025 11:07
@flying-sheep flying-sheep changed the title tSNE components parameter (feat): add n_components parameter to tSNE May 8, 2025
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flying-sheep merged commit c2a7a4b into scverse:main May 15, 2025
selmanozleyen pushed a commit that referenced this pull request May 19, 2025
Co-authored-by: Phil Schaf <flying-sheep@web.de>
ilan-gold added a commit that referenced this pull request May 19, 2025
* update normalize_total & remove dep

* refactor: `normalize_total` with Numba (#3593)

Co-authored-by: Philipp A. <flying-sheep@web.de>

* fix doctest

* add release note

* Switch from profimp to tuna for parsing import profiles (#3620)

* [pre-commit.ci] pre-commit autoupdate (#3622)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Philipp A. <flying-sheep@web.de>

* Fix typo (#3555)

Co-authored-by: Phil Schaf <flying-sheep@web.de>

* Switch to fast-array-utils (#3598)

Co-authored-by: Rodrigo Goya <rgoya@users.noreply.github.com>

* tSNE components parameter (#2803)

Co-authored-by: Phil Schaf <flying-sheep@web.de>

* Simplify scale (#3351)

Co-authored-by: Intron7 <severin.dicks@icloud.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* remove layers test

* explicit return and fix the info message

* remove unnecessary ravel's

* precision fix

* (fix): maintain data type properly.

* (fix): remove artifact storage

* (refactor): use nice f-a-u typing

---------

Co-authored-by: Philipp A. <flying-sheep@web.de>
Co-authored-by: Selman Özleyen <32667648+selmanozleyen@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Swastik Mishra <4453983+swstkm@users.noreply.github.com>
Co-authored-by: Rodrigo Goya <rgoya@users.noreply.github.com>
Co-authored-by: Kitsune <48340051+ch1ru@users.noreply.github.com>
Co-authored-by: selmanozleyen <syozleyen@gmail.com>
Co-authored-by: ilan-gold <ilanbassgold@gmail.com>
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Additional parameters in some functions - new functions

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