API

API#

Import Ocelli as:

import ocelli as oci

Data reading (read)#

ocelli.read.h5ad(filename)

Load an h5ad file

Preprocessing (pp)#

ocelli.pp.neighbors(adata[, x, n_neighbors, ...])

Nearest neighbors search

ocelli.pp.lda(adata[, x, out, n_components, ...])

Latent Dirichlet Allocation

ocelli.pp.generate_modalities(adata[, ...])

Generate topic-based modalities from unimodal data.

Tools (tl)#

ocelli.tl.modality_weights(adata[, ...])

Compute multimodal weights for each cell

ocelli.tl.scale_weights(adata, obs, modalities)

Scale multimodal weights for selected cells and modalities

ocelli.tl.MDM(adata[, n_components, ...])

Multimodal Diffusion Maps

ocelli.tl.imputation(adata[, t, kappa, ...])

Diffusion-based multimodal imputation.

ocelli.tl.neighbors_graph(adata, x[, ...])

Nearest neighbors-based graph construction

ocelli.tl.transitions_graph(adata, x, ...[, ...])

Transitions-based graph construction

ocelli.tl.fa2(adata[, graph, n_components, ...])

ForceAtlas2 dimensionality reduction

ocelli.tl.umap(adata[, x, n_components, ...])

UMAP dimensionality reduction

ocelli.tl.zscores(adata, markers[, x, vmin, ...])

Gene signature mean z-scores

ocelli.tl.louvain(adata[, x, out, ...])

Louvain clustering

ocelli.tl.projection(adata, x[, phi, theta, ...])

Graphical projection of 3D data to 2D

Plotting (pl)#

ocelli.pl.scatter(adata, x[, s, c, cdict, ...])

2D scatter plots

ocelli.pl.scatter_interactive(adata, x[, s, ...])

2D and 3D interactive scatter plots

ocelli.pl.violin(adata, groups, values[, ...])

Feature violin plots

ocelli.pl.bar(adata, groups, values[, ...])

Feature bar plots

ocelli.pl.projections(adata, x[, s, c, ...])

Project and visualize 3D data from multiple angles