nearest_neighbor_summary: Summarize nearest neighbor distances

Description Usage Arguments Value

View source: R/distance_helpers.R

Description

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.

Usage

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nearest_neighbor_summary(
  csd,
  phenotypes = NULL,
  categories = NA,
  details_path = NULL,
  .by = "Slide ID",
  extra_cols = NULL
)

Arguments

csd

Cell seg data with Cell X Position, Cell Y Position, field name and Phenotype columns.

phenotypes

Optional list of phenotypes to include. If omitted, will use unique_phenotypes(csd).

categories

Optional list of tissue categories to compute within. If omitted or NA, all cells will be included.

details_path

If present, path to save a tab-separated table for each tissue category containing nearest-neighbor data for each cell in the tissue category.

.by

Column to aggregate by

extra_cols

The names of extra columns to include in the detailed results.

Value

A data frame with summary statistics for each phenotype pair in each Slide ID for each tissue category.


akoyabio/phenoptrReports documentation built on Jan. 17, 2022, 6:22 p.m.