SC_2 preprocessing update proteomics - Githubissues

saeyslab / harpy

https://harpy.readthedocs.io/en/latest/

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SC_2 preprocessing update proteomics #2

Closed ArneDefauw closed 7 months ago

ArneDefauw commented 7 months ago

refactor preprocessing functions (sp.tb.preprocess_proteomics and sp.tb.preprocess_transcriptomics)

workflow as follows:

from sparrow.table._clustering import leiden
from sparrow.table._preprocess import preprocess_proteomics
sdata_multi_c = preprocess_proteomics(sdata_multi_c, labels_layer="masks_whole")
sdata_multi_c = leiden(sdata_multi_c, labels_layer="masks_whole", key_added="leiden", random_state=100)