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ebi-gene-expression-group / scanpy-scripts

Scripts for using scanpy
Apache License 2.0
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Feature/function improvements #41

Closed nh3 closed 5 years ago

nh3 commented 5 years ago

This PR adds trajectory-related functions sc.tl.paga(), sc.tl.diffmap(), sc.tl.dpt(), scatter plot function, and includes a set of bugfix and improvements of existing functions.

nh3 commented 5 years ago

They cover trajectory-related functions, but not scatter plots. I'm still a bit undecided whether to integrate plotting to calculation at the scripts level or at the galaxy wrapper level. The latter is more flexible but the former may save one IO.

pcm32 commented 5 years ago

This looks good for me to merge at the moment. I would keep certain plotting facilities, turnable on and off, within the script. It is nice for users in Galaxy I think.

pcm32 commented 5 years ago

Please merge at earliest convenience.

nh3 commented 5 years ago

I've added plotting as a separate command (with tests included) for now. Will implement the other strategy in another PR.