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Find better way to determine threshold of representative markers #1

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aathbt opened this issue Dec 19, 2023 · 0 comments
Open

Find better way to determine threshold of representative markers #1

aathbt opened this issue Dec 19, 2023 · 0 comments
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enhancement New feature or request

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aathbt commented Dec 19, 2023 •
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In identify_phenotypes.py, the threshold to check bimodality of the markers is a hard cap. Maybe this could be improved and automated.

Ideas:

  • Create plots for mean and variance distribution to let users how to adapt the threshold (not automated, but decision will be more informed)
  • Determine markers through quantile of cells satisfying some conditions, e.g marker expression < 3 in at least X% cells and marker expression > 3 in at least X% cells (more automated, but impact of X should be checked)
@aathbt aathbt added the enhancement New feature or request label Dec 19, 2023
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@bernibra @aathbt