import scanpy as sc
Data structure
image.png
Main API and it's logic
-
sc.pp.blabla
pp = preprocessing
perform a basic transformation on the data matrix, i.e., the numpy array .X. -
sc.tl.blabla
tl = tools
add annotation to the data, i.e., change pandas dataframe .var and .obs -
sc.pl.blabla
pl = plotting
plot function, largely parallels the tl.* and a few of the pp.* functions
other API can be found in references.
Discussion
This data structure is a very classical bioinformatic data structure, which ensembles some in Bioconductor.
References
https://scanpy.readthedocs.io/en/stable/basic_usage.html
