count_within_summary: Summarize "count within" distances
In akoyabio/phenoptrReports: Create reports using Phenoptics data

Description Usage Arguments Details Value

Computes summary "count within" statistics for each Slide ID in csd and each pair of phenotypes in phenotypes. See phenoptr::count_within() for details of the counts and the summary calculation.

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

`csd`	Cell seg data with `Cell X Position`, `Cell Y Position`, field name and `Phenotype` columns.
`radii`	Vector of radii to search within.
`phenotypes`	Optional list of phenotypes to include. If omitted, will use `unique_phenotypes(csd)`. Counts are computed for all pairs of phenotypes.
`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 tab-separated tables with count within data for each cell.
`.by`	Column to aggregate by
`extra_cols`	The names of extra columns to include in the detailed results.

If details_path is provided, this will save a table with one row per cell and columns for each phenotype and radius giving the count of cells of that type within that distance.

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.

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

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