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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
https://oncopathtk.org
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il2 importance analysis #264

Closed CarlinLiao closed 11 months ago

CarlinLiao commented 11 months ago

Merge to close #263.

CarlinLiao commented 11 months ago

I've implemented my addition in the pattern of the other analyses, but I'm getting a small error.

One of the custom phenotypes I'm using is a mixture of "simple" and "complex" phenotypes, ["Tumor", "MHCI"]. This causes an error because the phenotype-criteria API endpoint appears to be only set up to handle "complex" phenotypes, as "Tumor" is processed fine but "MHCI" causes a 500 internal server error. I can work around this, but I would think that this isn't necessarily desired behavior.

CarlinLiao commented 11 months ago

Once the above issue is resolved, this is ready to merge.

jimmymathews commented 11 months ago

Look at the other examples, for non-named phenotypes you have to specify a dict of postive_markers list and negative_markers list.

jimmymathews commented 11 months ago

Also the sequence of results computed here is supposed to match the manuscript narrative, not just list bulk results. So we should select the ones notable enough to have a sentence about them (and also write that sentence), including in this reproduction script in the same order that they appear in the narrative.

jimmymathews commented 11 months ago

Looks good.