User API

User API#

Import scviva-tools as:

import scviva

`model.SCVIVA`	scVIVA: variational auto-encoder with niche decoders for ST:cite:p:Levy25.
`model.DestVI`	Multi-resolution deconvolution of Spatial Transcriptomics data (DestVI) [Lopez et al., 2022].
`model.ResolVI`	ResolVI addresses noise and bias in single-cell resolved spatial transcriptomics data.
`model.GIMVI`	Joint VAE for imputing missing genes in spatial data [Lopez et al., 2019].

`external.RNAStereoscope`	Reimplementation of Stereoscope for the scRNA-seq component [Andersson et al., 2020].
`external.SpatialStereoscope`	Reimplementation of Stereoscope for the spatial component [Andersson et al., 2020].
`external.Tangram`	Torch reimplementation of Tangram [Biancalani et al., 2021].

Downstream spatial metabolic cell-cell communication analysis.

`pl.harreman.local_correlation_plot`	Plot a hierarchical-clustered heatmap of pairwise correlation Z-scores.
`pl.harreman.average_local_correlation_plot`	Plot the average pairwise correlation Z-scores between modules.
`pl.harreman.module_score_correlation_plot`	Plot correlations between module scores across cells.
`pl.harreman.plot_interacting_cell_scores`	Plot spatial maps of interacting cell scores for selected gene pairs or metabolites.
`pl.harreman.plot_ct_interacting_cell_scores`	Plot cell-type–specific interacting cell scores across spatial coordinates.
`pl.harreman.plot_interaction_module_correlation`	Plot interaction-module correlation heatmap.
`pl.plot_cell_type_map`	Plot spatial map of cell type proportion(s).
`pl.scviva_de.plot_niche_de_decision_boundary`	Plot the results of the niche differential expression analysis.
`pl.scviva_de.plot_connectivity_distribution`	Plot a histogram of the number of non-zero entries per row of a sparse matrix.

Config manager for scviva.