count_phenotypes: Count phenotypes per slide and tissue category

In akoyabio/phenoptrReports: Create reports using Phenoptics data

Description

Count selected phenotypes, aggregating by Slide ID and Tissue Category. If multiple tissue categories are selected, include a Total row for each Slide ID.

Usage

count_phenotypes(csd, phenotypes, tissue_categories, .by = "Slide ID")

Arguments

csd	Cell seg data to use. This should already have been filtered for the slides or fields of interest.
phenotypes	A named list of phenotype selectors (see phenoptr::parse_phenotypes). Results will be reported in the same order as phenotypes are listed here. To include a row total, phenotypes should contain a "Total" item.
tissue_categories	A character vector of tissue category names of interest.
.by	Column to aggregate by

Value

A data frame with columns for Slide ID, Tissue Category, cell counts for each requested phenotype, and total cells.

See Also

Other aggregation functions: compute_density_from_cell_summary(), compute_density_from_table(), compute_h_score_from_score_data(), compute_h_score(), compute_mean_expression_many(), compute_mean_expression(), compute_positivity_many(), compute_positivity(), counts_to_percents()

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