AUC_of_cross_function   The difference in AUC of the cross function
                        curves
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
R_BC                    The ratio of border cell count to cluster cell
                        count
select_celltypes        select_celltypes
simulated_image         SPE object of a formatted image (simulated by
                        'spaSim' package)
