API reference#

MechanoChat follows the Scanpy convention: import the package once and reach the three functional namespaces through their short aliases.

import os
os.environ["NUMBA_CUDA_USE_NVIDIA_BINDING"] = "1"   # see the installation page
import mechanochat as mc

Alias

Module

Purpose

—

mechanochat.SEM

SEM2 / SEM3 simulation classes

mc.pp

mechanochat.preprocessing

MechanoChatDB loading and signal preprocessing

mc.tl

mechanochat.tools

contact, force and communication inference

mc.pl

mechanochat.plotting

visualization

Results are written back into the AnnData object under .obsp, .obsm and .uns, so intermediate objects rarely need to be passed around by hand.