findCellTypesFromEnrichment

Source: R/spatial_enrichment_visuals.R

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.