Spatial Image Analysis of Tissues
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘SPIAT’ version 1.6.0
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) |