omicverse.single.TrajInfer

omicverse.single.TrajInfer#

class omicverse.single.TrajInfer(adata, basis='X_umap', use_rep='X_pca', n_comps=50, n_neighbors=15, groupby='clusters')[source]#

Trajectory inference class for single-cell data analysis.

This class provides methods for inferring developmental trajectories using various algorithms including Palantir, diffusion maps, and Slingshot.

Parameters:

  • adata (AnnData)

  • basis (str (default: 'X_umap'))

  • use_rep (str (default: 'X_pca'))

  • n_comps (int (default: 50))

  • n_neighbors (int (default: 15))

  • groupby (str (default: 'clusters'))

__init__(adata, basis='X_umap', use_rep='X_pca', n_comps=50, n_neighbors=15, groupby='clusters')[source]#

Initialize trajectory inference object.

Parameters:

  • adata (anndata.AnnData) – AnnData object containing single-cell expression and embeddings.

  • basis (str) – Embedding key in adata.obsm used for visualization (for example 'X_umap').

  • use_rep (str) – Representation key in adata.obsm used for trajectory inference.

  • n_comps (int) – Number of components from use_rep used for graph/diffusion computation.

  • n_neighbors (int) – Number of neighbors used in graph construction.

  • groupby (str) – Cluster/annotation key in adata.obs.

Methods

__init__(adata[, basis, use_rep, n_comps, ...])

Initialize trajectory inference object.

inference([method])

Perform trajectory inference using specified method.

palantir_cal_branch([plot_kwargs, return_fig])

Calculate and plot branch selection for Palantir results.

palantir_cal_gene_trends([layers])

Calculate gene expression trends along Palantir trajectories.

palantir_plot_gene_trends(genes[, lineages, ...])

Plot gene expression trends along Palantir trajectories.

palantir_plot_pseudotime([return_fig])

Plot Palantir pseudotime results.

set_origin_cells(origin)

Set origin cell type for trajectory inference.

set_terminal_cells(terminal)

Set terminal cell types for trajectory inference.
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