identify_cell_communities

Source: R/identify_cell_communities.R

Identifies communities of cells based on their location. It excludes cells without a phenotype

identify_cell_communities(
  sce_object,
  clustering_method = "dbscan",
  radius = NULL,
  min_community_size = 50,
  phenotypes_of_interest = NULL
)

Arguments

sce_object

SingleCellExperiment object in the form of the output of format_image_to_sce
clustering_method

String specifying which clustering algorithm to use. Current options: "dbscan" and "rphenograph"
radius

Integer specifying the radius of search. Required for "dbscan"
min_community_size

Minimum number of cells in a community
phenotypes_of_interest

Vector of phenotypes to consider

Value

A data.frame and a plot is returned