.aggregated_interaction_counts — .aggregated_interaction

Used when an informal analysis with sample groupings is specified to pairwiseAdjacency. Aggregates counts of each type of interaction across all Regions in a sample. Can also permute the cell type labels as needed for the "permutation" method of pairwiseAdjacency.

Usage

.aggregated_interaction_counts(
  cm,
  match_feature,
  feature_char,
  all_nns,
  nn,
  drop.self,
  permute_labels = FALSE
)

Arguments

cm: An object's cellMetadata
match_feature: A column in cm
feature_char: as.character(cm[match_feature]) passed in from pairwiseAdjacency
all_nns: A list of all the NN objects associated with a grouped analysis
nn: The name of a nearestNeighborGraph from object (character).
drop.self: If TRUE, ensures that the index cell is not counted as its own interaction, even if such self-interactions are present in the network-graph (NN object). This is recommended to be TRUE in almost all cases.
permute_labels: Whether to sample cell type labels before counting pairwise adjacencies.

Value

A table in the same format returned by count_pairwise_interactions