update pipeline

[michaelbornholdt]

modified from EmbeddedArtistry

Description

Updating the pipeline image after working on a new version for the LINCS repo.

What is the nature of your change?

• Bug fix (fixes an issue).
• Enhancement (adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

Checklist

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• I have read the CONTRIBUTING.md guidelines.
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[michaelbornholdt]

@niranjchandrasekaran Can you accept this. Or comment on the image if you want it changed.

[codecov-commenter]

Codecov Report

Merging #163 (fb7015b) into master (372f108) will decrease coverage by 0.01%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #163      +/-   ##
==========================================
- Coverage   98.09%   98.07%   -0.02%     
==========================================
  Files          49       52       +3     
  Lines        2253     2441     +188     
==========================================
+ Hits         2210     2394     +184     
- Misses         43       47       +4     

Flag	Coverage Δ
unittests	98.07% <ø> (-0.02%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
pycytominer/cyto_utils/cells.py	96.26% <0.00%> (-0.77%)	⬇️
pycytominer/tests/test_cyto_utils/test_util.py	96.89% <0.00%> (-0.40%)	⬇️
pycytominer/annotate.py	100.00% <0.00%> (ø)
pycytominer/aggregate.py	96.77% <0.00%> (ø)
pycytominer/normalize.py	100.00% <0.00%> (ø)
pycytominer/cyto_utils/__init__.py	100.00% <0.00%> (ø)
pycytominer/operations/__init__.py	100.00% <0.00%> (ø)
pycytominer/tests/test_feature_select.py	100.00% <0.00%> (ø)
pycytominer/operations/variance_threshold.py	97.05% <0.00%> (ø)
pycytominer/tests/test_cyto_utils/test_modz.py	100.00% <0.00%> (ø)
... and 10 more

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[niranjchandrasekaran]

@michaelbornholdt The old figure shows all the things that could be done using pycytominer (the figure will need to be updated once the Ruifan's feature selection methods are added) while the new figure is specific to how the LINCS dataset was processed. Is there a reason why you want to replace the general pipeline with the LINCS specific pipeline in this repo?

[michaelbornholdt]

Ah yes. You're totally right. I need to change that again then!

[michaelbornholdt]

@niranjchandrasekaran @gwaygenomics
Please look at this new image. It has been updated in accord to the one in the lincs repo

[gwaybio]

• I think you need to add Ruifan's method still
• Shouldn't data level 4bs also funnel to cytominer-eval?

[michaelbornholdt]

Dont know what is meant by Ruifans method.

And yes, I can link 4bs to cyto eval as well.

[gwaybio]

@ruifanp's method "noise_removal" added in #153 - please add it to the feature seleection method options

[michaelbornholdt]

@gwaygenomics Done now

[gwaybio]

perfect, i'll merge