Count cells within a radius for multiple tissue categories, phenotypes and fields.

This is a batch version of count_within. Given the path to a directory containing cell seg data files, for each given tissue category, pair of 'from' phenotype and 'to' phenotype, and radius, it counts the number of 'from' cells having a 'to' cell within radius microns.

count_within_batch(base_path, pairs, radius, category = NA,
  phenotype_rules = NULL, verbose = TRUE)

Arguments

base_path	Path to a directory containing at least one _cell_seg_data.txt file.
pairs	A list of pairs of phenotypes. Each entry is a two-element vector. The result will contain values for each pair.
radius	The radius or radii to search within.
category	Optional tissue categories to restrict both from and to phenotypes.
phenotype_rules	(Optional) A named list. Item names are phenotype names and must match entries in pairs. Item values are selectors for select_rows.
verbose	If TRUE, display progress.

Value

A data_frame containing these columns:

slide_id

Slide ID from the data files.

source

Base file name of the source file with _cell_seg_data.txt stripped off for brevity.

category

Tissue category, if provided as a parameter, or "all".

from

From phenotype.

to

To phenotype.

radius, from_count, to_count, from_with, within_mean

Results from count_within for this data file and tissue category.

Details

The category parameter may be a single category or a list of categories.

See the tutorial Selecting cells within a cell segmentation table for more on the use of pairs and phenotype_rules.

See also

Other distance functions: compute_all_nearest_distance, count_touching_cells, count_within, distance_matrix, find_nearest_distance, spatial_distribution_report, subset_distance_matrix

Examples

base_path <- sample_cell_seg_folder()

# Count tumor cells near macrophages, and tumor cells near CD8 separately,
# in tumor and stroma tissue categories separately.
pairs <- list(c('CK+', 'CD68+'),
             c('CK+', 'CD8+'))
radius <- c(10, 25)
category <- list('Tumor', 'Stroma')
count_within_batch(base_path, pairs, radius, category)
#> Processing Set4_1-6plex_[16142,55840] 
#> # A tibble: 8 x 10
#>   slide_id     source     categ~ from  to    radius from_c~ to_c~ from~ within~
#>   <chr>        <chr>      <chr>  <chr> <chr>  <dbl>   <int> <int> <int>   <dbl>
#> 1 Set4_1-6plex Set4_1-6p~ Tumor  CK+   CD68+   10.0    2192   101    79  0.0397
#> 2 Set4_1-6plex Set4_1-6p~ Tumor  CK+   CD68+   25.0    2192   101   397  0.308 
#> 3 Set4_1-6plex Set4_1-6p~ Tumor  CK+   CD8+    10.0    2192    51    63  0.0342
#> 4 Set4_1-6plex Set4_1-6p~ Tumor  CK+   CD8+    25.0    2192    51   320  0.203 
#> 5 Set4_1-6plex Set4_1-6p~ Stroma CK+   CD68+   10.0      65   316     6  0.0923
#> 6 Set4_1-6plex Set4_1-6p~ Stroma CK+   CD68+   25.0      65   316    34  0.785 
#> 7 Set4_1-6plex Set4_1-6p~ Stroma CK+   CD8+    10.0      65   177     4  0.0769
#> 8 Set4_1-6plex Set4_1-6p~ Stroma CK+   CD8+    25.0      65   177    22  0.600 

# Count tumor cells near any T cell in all tissue categories.
# Use `phenotype_rules` to define the T cell phenotype
pairs <- c('CK+', 'T cell')
rules <- list(
'T cell'=c('CD8+', 'FoxP3+'))
count_within_batch(base_path, pairs, radius, phenotype_rules=rules)
#> Processing Set4_1-6plex_[16142,55840] 
#> # A tibble: 2 x 10
#>   slide_id     source     categ~ from  to     radius from_~ to_c~ from~ within~
#>   <chr>        <chr>      <chr>  <chr> <chr>   <dbl>  <int> <int> <int>   <dbl>
#> 1 Set4_1-6plex Set4_1-6p~ all    CK+   T cell   10.0   2257   456   150  0.0762
#> 2 Set4_1-6plex Set4_1-6p~ all    CK+   T cell   25.0   2257   456   824  0.693