Files in TrigosTeam/SPIAT

Spatial Image Analysis of Tissues

NEWS.md R/AUC_of_cross_function.R R/R_BC.R R/SPIAT-package.R R/average_marker_intensity_within_radius.R R/average_minimum_distance.R R/average_nearest_neighbor_index.R R/average_percentage_of_cells_within_radius.R R/calculate_cell_proportions.R R/calculate_cross_functions.R R/calculate_distance_to_tumour_margin.R R/calculate_entropy.R R/calculate_minimum_distances_between_celltypes.R R/calculate_pairwise_distances_between_celltypes.R R/calculate_percentage_of_grids.R R/calculate_proportions_of_cells_in_structure.R R/calculate_spatial_autocorrelation.R R/calculate_summary_distances_between_celltypes.R R/calculate_summary_distances_of_cells_to_borders.R R/composition_of_neighborhoods.R R/compute_gradient.R R/crossing_of_crossK.R R/define_celltypes.R R/define_structure.R R/defined_image.R R/dimensionality_reduction_plot.R R/entropy_gradient_aggregated.R R/format_HALO_to_spe.R R/format_cellprofiler_to_spe.R R/format_codex_to_spe.R R/format_colData_to_spe.R R/format_image_to_spe.R R/format_inform_to_spe.R R/format_spe_to_ppp.R R/grid_metrics.R R/identify_bordering_cells.R R/identify_neighborhoods.R R/image_no_markers.R R/image_splitter.R R/marker_intensity_boxplot.R R/marker_prediction_plot.R R/marker_surface_plot.R R/marker_surface_plot_stack.R R/measure_association_to_cell_properties.R R/mixing_score_summary.R R/number_of_cells_within_radius.R R/plot_average_intensity.R R/plot_cell_categories.R R/plot_cell_distances_violin.R R/plot_cell_marker_levels.R R/plot_cell_percentages.R R/plot_composition_heatmap.R R/plot_distance_heatmap.R R/plot_marker_level_heatmap.R R/predict_phenotypes.R R/select_celltypes.R R/simulated_image.R R/utils.R README.md data-raw/defined_image.R data-raw/image_no_markers.R data-raw/simulated_image.R man/AUC_of_cross_function.Rd man/R_BC.Rd man/SPIAT-package.Rd man/average_marker_intensity_within_radius.Rd man/average_minimum_distance.Rd man/average_nearest_neighbor_index.Rd man/average_percentage_of_cells_within_radius.Rd man/calculate_cell_proportions.Rd man/calculate_cross_functions.Rd man/calculate_distance_to_margin.Rd man/calculate_entropy.Rd man/calculate_minimum_distances_between_celltypes.Rd man/calculate_pairwise_distances_between_celltypes.Rd man/calculate_percentage_of_grids.Rd man/calculate_proportions_of_cells_in_structure.Rd man/calculate_spatial_autocorrelation.Rd man/calculate_summary_distances_between_celltypes.Rd man/calculate_summary_distances_of_cells_to_borders.Rd man/composition_of_neighborhoods.Rd man/compute_gradient.Rd man/crossing_of_crossK.Rd man/define_celltypes.Rd man/define_structure.Rd man/defined_image.Rd man/dimensionality_reduction_plot.Rd man/entropy_gradient_aggregated.Rd man/format_cellprofiler_to_spe.Rd man/format_codex_to_spe.Rd man/format_colData_to_spe.Rd man/format_halo_to_spe.Rd man/format_image_to_spe.Rd man/format_inform_to_spe.Rd man/format_spe_to_ppp.Rd man/grid_metrics.Rd man/identify_bordering_cells.Rd man/identify_neighborhoods.Rd man/image_no_markers.Rd man/image_splitter.Rd man/marker_intensity_boxplot.Rd man/marker_prediction_plot.Rd man/marker_surface_plot.Rd man/marker_surface_plot_stack.Rd man/measure_association_to_cell_properties.Rd man/mixing_score_summary.Rd man/number_of_cells_within_radius.Rd man/plot_average_intensity.Rd man/plot_cell_categories.Rd man/plot_cell_distances_violin.Rd man/plot_cell_marker_levels.Rd man/plot_cell_percentages.Rd man/plot_composition_heatmap.Rd man/plot_distance_heatmap.Rd man/plot_marker_level_heatmap.Rd man/predict_phenotypes.Rd man/select_celltypes.Rd man/simulated_image.Rd tests/testthat.R tests/testthat/test-calculations.R tests/testthat/test-families.R tests/testthat/test-plotting.R tests/testthat/test-utilities.R vignettes/SPIAT.Rmd vignettes/basic_analysis.Rmd vignettes/cell-colocalisation.Rmd vignettes/data_reading-formatting.Rmd vignettes/neighborhood.Rmd vignettes/quality-control_visualisation.Rmd vignettes/spatial-heterogeneity.Rmd vignettes/tissue-structure.Rmd