findCellTypesFromEnrichment

findCellTypesFromEnrichment(
  gobject = NULL,
  spat_unit = NULL,
  feat_type = NULL,
  enrichment_name = "PAGE_z_score",
  return_frequency_table = FALSE
)

Arguments

gobject: Giotto Object
spat_unit: spatial unit in which the enrichment information is stored
feat_type: feature type for which the enrichment information was calculated
enrichment_name: name of the spatial enrichment i.e. output from GiottoClass::list_spatial_enrichment_names() Default value is "PAGE_Z_score"
return_frequency_table: see details. Default FALSE

Value

table

Details

This function returns a two-column matrix, one column will contain cell IDs and the other will contain the most likely cell type based on the provided enrichment.

By setting return_frequency_table to TRUE, a table will instead be returned. This table will detail the number of occurences for each cell type, based on the provided enrichment.

The cell types are assigned by determining the maximum value of the z-score or -log10(p-value) for a cell and the associated cell types from the enrichment.