Function reference • phenoptr

Package options
`phenoptr-package`	Helpers for working with inForm data
Read and preprocess inForm data and image files
`list_cell_seg_files()`	Find inForm data files.
`read_cell_seg_data()`	Read and clean an inForm data file.
`get_field_info()`	Read information about a field from a component image file.
`get_map_path()`	Get the path to the segmentation map file for a field
`read_components()`	Read a component TIFF file.
`read_composite_info()`	Read just the composite info from images in a TIFF composite image file.
`read_composites()`	Read composite images
`read_field_info()`	Read information about a field from a component image file.
`read_maps()`	Read an inForm segmentation map file.
`parse_tissue_description()`	Parse the description tag of the tissue map image read from an inForm `binary_seg_maps` file
Compute and visualize spatial relationships between cells
`find_nearest_distance()`	Nearest neighbor distances for each cell and phenotype.
`compute_all_nearest_distance()`	Nearest neighbors from a file.
`count_within()`	Count cells within a radius for a single field.
`count_within_batch()`	Count cells within a radius for multiple tissue categories, phenotypes and fields.
`count_within_detail()`	Compute count within for individual cells in a single field.
`count_within_many()`	Count cells within a radius for multiple tissue categories and phenotypes in a single field.
`count_touching_cells()`	Find and count touching cells for pairs of phenotypes.
`count_touching_cells_fast()`	Count touching cells for a single pair of phenotypes
`make_ppp()`	Make a marked point pattern for cells in a single field
`spatial_distribution_report()`	Create a spatial distribution report.
Estimate cell density
`density_bands()`	Estimate cell density in bands from a tissue boundary.
`density_at_distance()`	Estimate cell density at distance from a tissue boundary.
Helpers
`distance_matrix()`	Create a distance matrix from cell seg data.
`field_column()`	Get the name of the column that distinguishes fields in a merged cell seg data file.
`parse_phenotypes()`	Parse a vector of phenotype names
`phenotype_columns()`	Find the columns used by phenotype formulae
`plot_diverging()`	Plot a distance map using a diverging color scale with white at 0
`readTIFFDirectory()`	Read directory info from a TIFF file
`select_rows()`	Flexibly select rows of a data frame.
`subset_distance_matrix()`	Subset the rows and columns of a distance matrix.
`unique_phenotypes()`	Find unique phenotypes in a cell seg table
`validate_phenotype_definitions()`	Validate a user-specified phenotype definition
`validate_phenotypes()`	Validate a phenotype parameter
Sample data
`sample_cell_seg_data` `sample_cell_seg_path()` `sample_cell_seg_folder()`	Sample cell segmentation data.

Reference

Package options

Read and preprocess inForm data and image files

Compute and visualize spatial relationships between cells

Estimate cell density

Helpers

Sample data