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BodenmillerGroup / cytomapper

R package for visualization of highly multiplexed imaging data
https://bodenmillergroup.github.io/cytomapper/
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Started draft for bug fix #86

Open nilseling opened 11 months ago

nilseling commented 11 months ago

This is the start of the bug fix to address #85

This needs to be properly tested and adjusted. I already noticed now that when setting a gate that contains 0 cells leads to the clearing of all subsequent gates. This has not been the behaviour before the fix.

codecov[bot] commented 11 months ago

Codecov Report

Attention: 46 lines in your changes are missing coverage. Please review.

Comparison is base (7ba413f) 87.31% compared to head (adaae45) 87.06%.

Files Patch % Lines
R/server-utils.R 9.80% 46 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #86 +/- ## ========================================== - Coverage 87.31% 87.06% -0.25% ========================================== Files 18 18 Lines 2751 2761 +10 ========================================== + Hits 2402 2404 +2 - Misses 349 357 +8 ```

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nilseling commented 11 months ago

I introduced a few more fixes:

  1. when the assay changed, the first gate was not erased (now fixed)
  2. There was a strange bug that when the first marker of a gate was set to empty, the gate was not erased. For safety reasons I have now added that all gates and objects are erased when any marker changes.

@lassedochreden, @SchulzDan please test this in detail when you get the chance. The design choices and expectations are a bit complex to handle alone.

nilseling commented 11 months ago

Bzw, the build issues on devel seem to be slang related; see Bioc developers forum slack

SchulzDan commented 6 months ago

Hi, I just installed version 1.15.3 and it seems that empty gates still propagate the previous gate into the downloaded sce.