Make a marked point pattern for cells in a single field

Source: R/spatial_helpers.R

Makes a marked point pattern (spatstat.geom::ppp) for the cells of the specified phenotype in the specified tissue categories and field.

make_ppp(csd, export_path, pheno, field_name = NULL, tissue_categories = NULL)

Arguments

csd

Cell seg data, may contain multiple fields

export_path

Path to a directory containing composite and component image files from inForm

pheno

Phenotype definition. Either a (possibly named) character vector to be parsed by parse_phenotypes() or a named list containing a single phenotype definition as used by select_rows().

field_name

Sample Name or Annotation ID for the field of interest. May be omitted if csd contains data for only one field.

tissue_categories

Tissue categories of interest. If supplied, the returned ppp will contain only cells in these categories and the associated window will be restricted to the extent of these categories.

Value

Returns a marked point pattern (spatstat.geom::ppp object) with a single mark value.

Examples

# ppp for CD8+ cells in the sample data
suppressPackageStartupMessages(library(spatstat))
pp <- make_ppp(sample_cell_seg_data, sample_cell_seg_folder(),
  "CD8+", tissue_categories="Tumor")
#> Warning: 6 points were rejected as lying outside the specified window
plot(pp, show.window=FALSE, main='')
#> Warning: 6 illegal points also plotted


# To include multiple phenotypes in a single point pattern,
# create them separately and join them with [spatstat.geom::superimpose()].

pp2 <- make_ppp(sample_cell_seg_data, sample_cell_seg_folder(),
  "CK+", tissue_categories="Tumor")
#> Warning: 13 points were rejected as lying outside the specified window
plot(superimpose(pp2, pp), cols=c('red', 'blue'), show.window=FALSE, main='')