sample_cell_seg_data: Sample cell segmentation data.

In akoyabio/phenoptr: inForm Helper Functions

Description

A dataset containing inForm cell segmentation data for a single field.

Usage

sample_cell_seg_data

sample_cell_seg_path()

sample_cell_seg_folder()

Format

A data frame with 6072 rows and 199 variables

Details

sample_cell_seg_data contains the data_table returned from

read_cell_seg_data(sample_cell_seg_path())

This table shows the stains used, the epitopes they were bound to, and the colors used to show the stains in the composite and phenotype views.

  Stain    Epitope  Composite  Phenotype
  -------- -------  ---------  ---------
  DAPI     Nucleus  Blue       N/A
  Opal520  PDL1     Red        N/A
  Opal540  CD8      Yellow     Yellow
  Opal570  FoxP3    Orange     Orange
  Opal620  CD68     Magenta    Magenta
  Opal650  PD1      Green      N/A
  Opal690  CK       Cyan       Cyan

The sample cell data includes phenotypes CD8+ (cytotoxic T cell), CD68+ (macrophage), FoxP3+ (regulatory T cell), CK+ (tumor), and other.

sample_cell_seg_path and sample_cell_seg_folder are convenience functions which return the path to the sample cell seg file included in this package, or the folder containing sample cell seg data, respectively.

To see all the files included for this field, use list.files(sample_cell_seg_folder()).

For more sample data from this and related samples, see the phenoptrExamples package.

Examples

dim(sample_cell_seg_data)
table(sample_cell_seg_data$Phenotype)

akoyabio/phenoptr documentation built on Jan. 7, 2022, 5:37 p.m.