Example of using CAT without cli

Example of using CAT without cli#

import cat
from cat.dataset import Dataset
from cat.report import generate_tables

  1. Load datasets and specify required parameters

ds1 = Dataset(name="DS1", filename="./tests/datasets/mock.h5ad")
ds1.prepare(group_by="Condition_E+D", gene_symbol_field=None)

ds2 = Dataset(name="DS2", filename="./tests/datasets/mock.h5ad")
ds2.prepare(group_by="Condition_E+D", gene_symbol_field=None)

  1. Use CAT to preprocess the datasets by normalizing the datasets.

ds1, ds2 = cat.internal_preprocessing(ds1, ds2, features_file=None)

  1. Calculate pairwise differences

diff = cat.compare(ds1, ds2, n_iterations=1_000, distance="euclidean")

  1. Generate results in printable ways

tables = generate_tables(diff, 1.6)

print(tables)