tacco.tools.annotate_RCTD

annotate_RCTD(adata, reference, annotation_key, counts_location=None, conda_env=None, x_coord_name='x', y_coord_name='y', doublet=False, min_ct=0, UMI_min_sigma=None, n_cores=None, working_directory=None, verbose=True)[source]

Annotates an AnnData using reference data by RCTD [Cable21].

This is the direct interface to this annotation method. In practice using the general wrapper annotate() is recommended due to its higher flexibility.

Parameters:

  • adata – An AnnData including expression data in .X.

  • reference – Reference data to get the annotation definition from.

  • annotation_key – The .obs key where the annotation is stored in the reference. If None, it is inferred from reference, if possible.

  • counts_location – A string or tuple specifying where the count matrix is stored, e.g. ‘X’, (‘raw’,’X’), (‘raw’,’obsm’,’my_counts_key’), (‘layer’,’my_counts_key’), … For details see counts().

  • conda_env – The path of a conda environment where RCTD is installed and importable as ‘library(RCTD)’.

  • x_coord_name – Name of an .obs column to forward to RCTD as x coordinates. If not available, forwards a new 0-only column.

  • y_coord_name – Name of an .obs column to forward to RCTD as y coordinates. If not available, forwards a new 0-only column.

  • doublet – Whether to run in “doublet” mode. Alternative is “full” mode.

  • min_ct – Minimum number of cells in a group to include in the RCTD run.

  • UMI_min_sigma – As default, RCTD has this value at 300, which is quite large for some datasets, and breaks RCTD. Therefore the default heuristic for None here is at min(300,median(total_counts_per_observation)-1). See RCTD docs for details about this parameter.

  • n_cores – Number of cores to use for RCTD. If None, use all available cores.

  • working_directory – The directory where to store all the intermediates. If None, a temporary directory is used and cleaned in the end. This option is probably only relevant for debugging.

  • verbose – Whether to print stderr and stdout of the RCTD run.

Returns:

Returns the annotation in a DataFrame.