Function reference • SPIAT

All functions
`AUC_of_cross_function()`	The difference in AUC of the cross function curves
`R_BC()`	The ratio of border cell count to cluster cell count
`average_marker_intensity_within_radius()`	average_marker_intensity_within_radius
`average_minimum_distance()`	average_minimum_distance
`average_nearest_neighbor_index()`	Average nearest neighbor index for point pattern (clustering or dispersion)
`average_percentage_of_cells_within_radius()`	average_percentage_of_cells_within_radius
`calculate_cell_proportions()`	calculate_cell_proportions
`calculate_cross_functions()`	calculate_cross_functions
`calculate_distance_to_margin()`	calculate the distances of each cell to the margin
`calculate_entropy()`	calculate_entropy
`calculate_minimum_distances_between_celltypes()`	calculate_minimum_distances_between_celltypes
`calculate_pairwise_distances_between_celltypes()`	calculate_pairwise_distances_between_celltypes
`calculate_percentage_of_grids()`	calculate_percentage_of_grids
`calculate_proportions_of_cells_in_structure()`	calculate_proportions_of_cells_in_structure
`calculate_spatial_autocorrelation()`	calculate_spatial_autocorrelation
`calculate_summary_distances_between_celltypes()`	calculate_summary_distances_between_celltypes
`calculate_summary_distances_of_cells_to_borders()`	calculate_summary_distances_of_cells_to_borders
`composition_of_neighborhoods()`	composition_of_neighborhoods
`compute_gradient()`	compute_gradient
`crossing_of_crossK()`	crossing_of_crossK
`define_celltypes()`	define_celltypes
`define_structure()`	define_structure
`defined_image`	SPE object of a simulated image with defined cell types based on marker combinations.
`dimensionality_reduction_plot()`	Dimensionality reduction plot
`entropy_gradient_aggregated()`	The aggregated gradient of entropy and the peak of the gradient
`format_cellprofiler_to_spe()`	Format a cellprofiler image into a SpatialExperiment object
`format_codex_to_spe()`	Format a CODEX image into a SpatialExperiment object
`format_colData_to_spe()`	format_colData_to_spe
`format_halo_to_spe()`	Format a HALO image into a SpatialExperiment object
`format_image_to_spe()`	Format an image into a SpatialExperiment object
`format_inform_to_spe()`	Format an inForm image into a SpatialExperiment object
`format_spe_to_ppp()`	Format SPE object as a ppp object (`spatstat` package)
`grid_metrics()`	Split an image into grid and calculates a metric for each grid square
`identify_bordering_cells()`	identify_bordering_cells
`identify_neighborhoods()`	identify_neighborhoods
`image_no_markers`	SPE object of a formatted image without marker intensities (simulated by `spaSim` package)
`image_splitter()`	Split a large image into sub images
`marker_intensity_boxplot()`	marker_intensity_boxplot
`marker_prediction_plot()`	marker_prediction_plot
`marker_surface_plot()`	marker_surface_plot
`marker_surface_plot_stack()`	marker_surface_plot_stack
`measure_association_to_cell_properties()`	measure_association_to_cell_properties
`mixing_score_summary()`	Calculate the (normalised) mixing score for interested cell types
`number_of_cells_within_radius()`	Number of cells within a radius
`plot_average_intensity()`	plot_average_intensity
`plot_cell_categories()`	plot_cell_categories
`plot_cell_distances_violin()`	plot_cell_distances_violin
`plot_cell_marker_levels()`	plot_cell_marker_levels
`plot_cell_percentages()`	plot_cell_percentages
`plot_composition_heatmap()`	plot_composition_heatmap
`plot_distance_heatmap()`	plot_distance_heatmap
`plot_marker_level_heatmap()`	plot_marker_level_heatmap
`predict_phenotypes()`	predict_phenotypes
`select_celltypes()`	select_celltypes
`simulated_image`	SPE object of a formatted image (simulated by `spaSim` package)

Reference

All functions