This function builds files needed for hierarchical mapping and stores them in the uns$hierarchical of AIT (Shiny) taxonomy.
addMapMyCells.RdThis hierarchical mapping is a wrapper around cell_type_mapper and call's it's functions to generate needed files needed for mapping.
Usage
addMapMyCells(
AIT_anndata,
hierarchy = AIT_anndata$uns$hierarchy,
anndata_path = NULL,
force = FALSE,
n_processors = 3,
normalization = "log2CPM",
tmp_dir = NULL,
user_precomp_stats_path = NULL,
user_query_markers_path = NULL
)Arguments
- AIT_anndata
A reference taxonomy anndata object.
- hierarchy
Named list of term_set_labels in the reference taxonomy ordered from most gross to most fine. Will default to list included in AIT_anndata, if any. E.g. "Class" = 0, "Subclass"= 1
- anndata_path
Local file path of the AIT reference taxonomy (h5ad file).
- force
Boolean value indicating whether to overwrite the AIT reference taxonomy's hierarchical file for a given mode.
- n_processors
Number of independent worker processes to spin up.
- normalization
Normalization of the h5ad files; must be either 'raw' or 'log2CPM'.
- tmp_dir
Temporary directory for writing out the hierarchical files.
- 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.