Loading CCI results

This tutorial shows how to load CCI results from different CCI tools

import mmcci

stLearn

We can load stLearn outputs from the path of the h5ad file that has been run through stLearn

stlearn = mmcci.io.read_stLearn('/path/to/stLearn.h5ad')

We can also convert AnnData objects that have been processed with stLearn

stlearn = mmcci.io.convert_stLearn(adata)

We can load CellPhoneDB outputs from the interaction scores text file

cellphonedb = mmcci.io.read_CellPhoneDB('/path/to/interaction_scores.txt')

We can load Squidpy results from running squidpy.gr.ligrec, which is a Python dict. This can be saved as a pkl file and loaded in.

import pickle

with open('/path/to/squidpy_dict.pkl', 'rb') as f:
    squidpy_dict = pickle.load(f)

squidpy = mmcci.io.read_Squidpy(squidpy_dict)

You can also load single networks such as squidpy.gr.interaction_matrix

squidpy = mmcci.io.read_network('/path/to/network.csv')

We can load CellChat outputs from the path of the cellchat_out@dr, saved as a csv file.

cellchat = mmcci.io.read_CellChat('/path/to/cellchat_dr.csv')

We can load NATMI outputs from the Edges_lrc2p.csv file that is outputted from NATMI

natmi = mmcci.io.read_NATMI('/path/to/Edges_lrc2p.csv')