Velocity Label Transfer

Python function that calls tangram to transfer velocity clusters to their spatial contexts.

Usage

velocity_label_transfer(
  adata,
  adata_st,
  velocity_cluster_key = "velocity_cluster",
  tangram_result_column = "velocity_label_transfer",
  plot = None
)

Arguments

adata

A single-cell RNAseq anndata object that contains velocities.

adata_st

A single-cell spatial RNA-seq object, preferably containing similar cells as adata, to which the velocity clusters labels will be transferred to via the package tangram-sc.

velocity_cluster_key

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

tangram_result_column

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

plot

default None. If you would like to save the plot, type in a string denoting the filename e.g. plot = plot.png