This function maps query data against the AIT (Shiny) reference taxonomy using hierarchical mapping.

This function maps query data against the AIT (Shiny) reference taxonomy using hierarchical mapping.

hierarchicalMapMyCells(
  AIT_anndata,
  query_data,
  mapping_params_list = list(),
  flat_mapping = FALSE,
  tmp_dir = NULL,
  user_extended_result_path = NULL,
  user_precomp_stats_path = NULL,
  user_query_markers_path = NULL
)

Arguments

AIT_anndata

A reference taxonomy anndata object.

query_data

A logCPM normalized matrix to be annotated.

tmp_dir

Temporary directory for writing out the hierarchical files.

user_extended_result_path

Full file path and name where the original mapping results will be saved.

user_precomp_stats_path

Alternative path to the user provided precompute stats HDF5 file. Will be generated, if not provided.

user_query_markers_path

Alternative path to the user provided query markers JSON file. Will be generated, if not provided.

Note: this hierarchical mapping is a wrapper around cell_type_mapper, and call's it's functions to generate needed files needed for mapping.

chunk_size

Number of rows each worker process should load at a time from the query dataset.

n_processors

Number of independent worker processes to spin up.

normalization

Normalization of the h5ad files; must be either 'raw' or 'log2CPM'.

Value

List of mapping results with labels and scores.