Compute cell densities from counts and tissue area — compute_density_from_cell_summary • phenoptrReports

Compute cell density from a table of cell counts and tissue areas read from a summary cell seg data file.

compute_density_from_cell_summary(
  counts,
  summary_path,
  tissue_categories,
  pixels_per_micron = getOption("phenoptr.pixels.per.micron"),
  .by = "Slide ID"
)

Arguments

counts: A data frame with columns for .by, Tissue Category, and counts, such as the output of count_phenotypes.
summary_path: Path(s) to cell seg data summary table(s) containing sample names and tissue categories matching counts.
tissue_categories: A character vector of tissue category names of interest.
pixels_per_micron: Conversion factor to microns.
.by: Column to aggregate by

Value

A data table with counts converted to density in \(cells / mm^2\).

See also

Other aggregation functions: 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(), count_phenotypes(), counts_to_percents()