Computes summary nearest neighbor statistics (mean, median, etc)
for each .by in csd and each pair of phenotypes in phenotypes.
Statistics are computed separately for each category in categories
and, if multiple categories are provided, once for all included cells.
Note: If categories is NA or includes NA, the "All" tissue category in
the results will include all cells in csd. If categories does not include
NA, the "All" tissue category will include only cells in the provided
categories.
nearest_neighbor_summary(
csd,
phenotypes = NULL,
categories = NA,
details_path = NULL,
.by = "Slide ID",
extra_cols = NULL
)Cell seg data with Cell X Position,
Cell Y Position, field name and Phenotype columns.
Optional list of phenotypes to include. If omitted,
will use unique_phenotypes(csd).
Optional list of tissue categories to compute within. If
omitted or NA, all cells will be included.
If present, path to save a tab-separated table for each tissue category containing nearest-neighbor data for each cell in the tissue category.
Column to aggregate by
The names of extra columns to include in the detailed results.
A data frame with summary statistics for each phenotype pair in each Slide ID for each tissue category.