# Spatial Image Analysis of Tissues

## Documentation for package ‘SPIAT’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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
defined_image | SPE object of a simulated image with defined cell types based on marker combinations.
define_celltypes | define_celltypes
define_structure | define_structure
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)
SPIAT | SPIAT: A package for spatial image analysis of tissues