celldancer.export_velocity_to_dynamo

celldancer.export_velocity_to_dynamo(cellDancer_df, adata)

Replace the velocities in adata of dynamo (“adata” in parameters) with the cellDancer predicted velocities (“cellDancer_df” in parameters). The output can be directly used in the downstream analyses of dynamo.

The vector field could be learned by dynamo based on the RNA velocity of cellDancer. Details are shown in the section ‘Application of dynamo.’

dynamo_vector_field_pancreas
Parameters

  • cellDancer_df (pandas.DataFrame) –

    The output dataframe of cellDancer.

    cellDancer –> dynamo

    bools of the existance of cellDancer_df[‘gene_name’] in adata.var –> adata.var[‘use_for_dynamics’]

    bools of the existance of cellDancer_df[‘gene_name’] in adata.var –> adata.var[‘use_for_transition’]

    cellDancer_df.splice_predict - cellDancer_df.splice –> adata.layers[‘velocity_S’]

  • adata (anndata._core.anndata.AnnData) – The adata to be integrated with cellDancer velocity result.

Return type

adata