A dataset containing inForm cell segmentation data for a single field.
sample_cell_seg_data sample_cell_seg_path() sample_cell_seg_folder()
A data frame with 6072 rows and 199 variables
sample_cell_seg_data contains the
data_table returned from
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),
FoxP3+ (regulatory T cell),
CK+ (tumor), and
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
For more sample data from this and related samples, see the phenoptrExamples package.
dim(sample_cell_seg_data)#>  6072 199table(sample_cell_seg_data$Phenotype)#> #> CD68+ CD8+ CK+ FoxP3+ other #> 417 228 2257 228 2942