identify_cell_clusters

Source: R/identify_cell_clusters.R

Uses Euclidean distances to identify clusters of cells within a specified radius.

identify_cell_clusters(
  sce_object,
  cell_types_of_interest,
  radius,
  column,
  no_pheno = NULL
)

Arguments

sce_object

SingleCellExperiment object in the form of the output of format_image_to_sce
cell_types_of_interest

Vector of phenotypes to consider
radius

Integer specifying the radius of search.
column

Column from which the cell types are selected
no_pheno

Cell type corresponding to cells without a known phenotype (e.g. "None", "Other")

Value

A data.frame and a plot is returned