add control exclusion and subsampling to 'prepare_checkpoint1()'

UCSF-DSCOLAB / cyclone

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add control exclusion and subsampling to 'prepare_checkpoint1()' #7

Closed dtm2451 closed 2 years ago

dtm2451 commented 2 years ago

Adds functionality for some missing "Data processing related" inputs into the prepare_checkpoint1() function.

These steps normally happen in step 1 of the pipeline, which the prepare_checkpoint1() functions aims to recreate for users whose data is already in matrix form rather than raw .fcs files.

Also updates:

[x] documentation formatting for prepare_checkpoint1()
[x] Subsampling process of the main pipeline to not use replacement

dtm2451 commented 2 years ago

Pretty ready from my perspective, although I haven't actually tested the subsampling change in the main pipeline.