YosefLab / Cassiopeia

A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction
https://cassiopeia-lineage.readthedocs.io/en/latest/
MIT License
77 stars 24 forks source link

speed up compute_dissimilarity_map #180

Closed Lioscro closed 1 year ago

Lioscro commented 2 years ago

Speed up cas.data.CassiopeiaTree.compute_dissimilarity_map by only computing dissimilarities between unique states first, and then expanding the dissimilarity map back to all cells.

codecov[bot] commented 2 years ago

Codecov Report

Patch coverage: 100.00% and project coverage change: +0.03% :tada:

Comparison is base (7a2db62) 79.49% compared to head (0a1b2c0) 79.53%. Report is 1 commits behind head on master.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #180 +/- ## ========================================== + Coverage 79.49% 79.53% +0.03% ========================================== Files 89 89 Lines 7916 7931 +15 ========================================== + Hits 6293 6308 +15 Misses 1623 1623 ``` | [Files Changed](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/180?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab) | Coverage Δ | | |---|---|---| | [cassiopeia/data/CassiopeiaTree.py](https://app.codecov.io/gh/YosefLab/Cassiopeia/pull/180?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=YosefLab#diff-Y2Fzc2lvcGVpYS9kYXRhL0Nhc3Npb3BlaWFUcmVlLnB5) | `91.76% <100.00%> (+0.18%)` | :arrow_up: |

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