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, if available.

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    category from  to    radius from_count to_count from_with
#>   <chr>     <chr>     <chr>    <chr> <chr>  <dbl>      <int>    <int>     <int>
#> 1 Set4_1-6~ Set4_1-6~ Tumor    CK+   CD68+    10.       2192      101        79
#> 2 Set4_1-6~ Set4_1-6~ Tumor    CK+   CD68+    25.       2192      101       397
#> 3 Set4_1-6~ Set4_1-6~ Tumor    CK+   CD8+     10.       2192       51        63
#> 4 Set4_1-6~ Set4_1-6~ Tumor    CK+   CD8+     25.       2192       51       320
#> 5 Set4_1-6~ Set4_1-6~ Stroma   CK+   CD68+    10.         65      316         6
#> 6 Set4_1-6~ Set4_1-6~ Stroma   CK+   CD68+    25.         65      316        34
#> 7 Set4_1-6~ Set4_1-6~ Stroma   CK+   CD8+     10.         65      177         4
#> 8 Set4_1-6~ Set4_1-6~ Stroma   CK+   CD8+     25.         65      177        22
#> # ... with 1 more variable: within_mean <dbl>

# 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    category from  to    radius from_count to_count from_with
#>   <chr>     <chr>     <chr>    <chr> <chr>  <dbl>      <int>    <int>     <int>
#> 1 Set4_1-6~ Set4_1-6~ all      CK+   T ce~    10.       2257      456       150
#> 2 Set4_1-6~ Set4_1-6~ all      CK+   T ce~    25.       2257      456       824
#> # ... with 1 more variable: within_mean <dbl>