celldancer.embedding_kinetic_para

celldancer.embedding_kinetic_para(cellDancer_df, kinetic_para, umap_n=25)

Calculate the UMAP based on the kinetic parameter(s).

Parameters
  • cellDancer_df (pandas.DataFrame) – Dataframe of velocity estimation results. Columns=[‘cellIndex’, ‘gene_name’, ‘unsplice’, ‘splice’, ‘unsplice_predict’, ‘splice_predict’, ‘alpha’, ‘beta’, ‘gamma’, ‘loss’, ‘cellID’, ‘clusters’, ‘embedding1’, ‘embedding2’]

  • kinetic_para (str) – Choose Which parameter is used to calculate embedding space, which could be selected from {‘alpha’, ‘beta’, ‘gamma’, ‘alpha_beta_gamma’}.

  • umap_n (optional, int (default: 25)) – The size of the local neighborhood (in terms of the number of neighboring sample points) used for manifold approximation in UMAP.

Returns

cellDancer_df – The updated cellDancer_df with an additional column of UMAP based on the kinetic parameter(s).

Return type

pandas.DataFrame