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broadinstitute / pooled-cell-painting-profiling-recipe

:woman_cook: Recipe repository for image-based profiling of Pooled Cell Painting experiments
BSD 3-Clause "New" or "Revised" License
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Adding aggregation step to generate profile module #9

Closed gwaybio closed 4 years ago

gwaybio commented 4 years ago

This script is the next downstream step after #8 and uses pycytominer.aggregate().

Currently, the output of this script (using CP074A as an example) are two files:

  1. Gene aggregation (592KB)
  2. Guide aggregation (2.4MB)
ErinWeisbart commented 4 years ago

This calls config["aggregate"] but that's not in this PR. Should it be?

gwaybio commented 4 years ago

This calls config["aggregate"] but that's not in this PR. Should it be?

Great catch. It should be... yes, note that I did the lazy thing and added the aggregate config options in https://github.com/broadinstitute/pooled-cell-painting-profiling-recipe/pull/8/commits/e606fe12d925d2aa4b046e4728452cec5aaa2640#diff-04ba2a82a13772907c6597e5ae1f54f2R53-R66

The "lazy" part means that we won't have to deal with merge conflicts by two pull requests dealing with the same file changing. In general, github makes merging nearly a non-trivial problem (and this ease of asynchronous development is one of the reasons github is so great!). (It can get VERY messy too - just something to be mindful of)

gwaybio commented 4 years ago

thanks for this succinct review @ErinWeisbart - ready for your re-review when you get a chance!