mean_of_top_and_bottom_cells: Compute mean expression levels of the top and bottom...

In akoyabio/phenoptrReports: Create reports using Phenoptics data

Description

Report the results in an Excel workbook in the same directory as csd_path.

Usage

mean_of_top_and_bottom_cells(
  csd_path = NULL,
  expression_cols,
  top_count = 20,
  bottom_percentile = 0.1,
  adjacent_max = 3,
  tissue_categories = NULL,
  .by = "Slide ID",
  out_path = NULL
)

Arguments

csd_path	Path to a merged cell seg data, or NULL. If NULL, a file chooser is opened to allow file selection.
expression_cols	Vector of column names to report.
top_count	The number of top-expressing cells to select for averaging.
bottom_percentile	The cutoff for the bottom percentile cells.
adjacent_max	The maximum ratio between expression of adjacent fluors
tissue_categories	Tissue categories to include, or NULL for all
.by	The column to aggregate by
out_path	The path to the output file; if NULL, a date-stamped file will be written to the same directory as csd_path.

Value

The path to the generated file.

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