Spatial Velocity Entrain Analysis

Python function takes in a dataset containing velocities, an accompanying spatially resolved dataset, and predicts ligands in spatial proximity that may be driving the observed velocities.

Usage

get_velocity_ligands_spatial(
  adata,
  adata_st,
  velocity_cluster_key = "velocity_clusters",
  vclusters = None,
  ligand_target_matrix = None,
  tangram_result_column = "velocity_label_transfer",
  expression_proportion_cutoff = 0.05,
  organism = "human",
  n_jobs = 4,
  n_top_genes = None
)

Arguments

adata

An anndata object containing velocities calculated with scvelo

adata_st

An anndata object containing spatially resolved data.

velocity_cluster_key

Column name in adata.obs denoting velocities clustered by entrain.cluster_velocities()

vclusters

Default None. If you would like to limit the analysis to a set of velocity clusters, you can define them here as an array.

ligand_target_matrix

NicheNet database

tangram_result_column

Default "velocity_label_transfer". Name of the column in adata where we will put the results of the label transfer.

expression_proportion_cutoff

Default 0.05. Population fraction threshold for including a ligand or receptor for Entrain analysis. A ligand or receptor is only included in analysis if it is expressed above this proportion. Specifically, if this is set to 0.05, a ligand or receptor is included in analysis if it has > 0 counts in 5% of cells in adata.X, where adata is subset to the cells belonging to the velocity cluster (for receptors); or spots belonging to the immediate spatial environment of the velocity cluster (for ligands).

organism

Default "human". Either one of "human" or "mouse". This argument feeds into omnipath-pypath module to convert human genes into mouse genes, if "mouse" is specified.

n_jobs

Default 4. Number of parallel jobs to use for scvelo.tl.recover_dynamics()

n_top_genes

Default None. Number of top velocity genes to consider for each cluster for scvelo.tl.recover_dynamics().

Value

An anndata object with Entrain results in anndata.uns