API

Import topomics as:

import topomics as tp

Models

models.MultimodalAmortizedLDA	Multimodal Amortized LDA with Mixture-of-Experts (MoE)
models.ShareTopic_LDA_Multi	Multimodal LDA with SHARE-Topic sparse ATAC Gibbs sampler.
models.SVEM_LDA_Multi	Stochastic Variational EM for MuData with shared topics across modalities.
models.BaseTopicModel	Base class for all models in the topomics package.

Preprocessing

pp.basic_preproc	Run a basic preprocessing on the AnnData object.
pp.elaborate_example	A method with a more complex docstring.

Tools

tl.basic_tool

Run a tool on the AnnData object.

Plotting

pl.basic_plot	Generate a basic plot for an AnnData object.
pl.spatial	A faster simple function that uses sc.pl.embedding to plot for non-visium data so it dont take too long.