|
AUC_of_cross_function()
|
AUC_of_cross_function |
|
average_marker_intensity_within_radius()
|
average_marker_intensity_within_radius |
|
average_minimum_distance()
|
average_minimum_distance |
|
average_nearest_neighbor_index()
|
average_nearest_neighbor_index |
|
average_percentage_of_cells_within_radius()
|
average_percentage_of_cells_within_radius |
|
bivariate_dependence()
|
bivariate_dependence |
|
calculate_all_distances_between_cell_types()
|
calculate_all_distances_between_cell_types |
|
calculate_cell_proportions()
|
calculate_cell_proportions |
|
calculate_cross_functions()
|
calculate_cross_functions |
|
calculate_cross_k_function()
|
Perform cross-K function |
|
calculate_cross_k_multiple_images()
|
Calculate K-cross function for multiple images and plot |
|
calculate_k_cross_function()
|
Perform cross-K function |
|
calculate_k_function()
|
calculate_k_function, calculates Ripley's K-function with border correction
with options to specify cell phenotype, plot, plot confidence envelope and plot confidence interval
of K function. Plotted K-functions utilise an inhomogenous Poisson distrubution with
point intensity produced to reflect the original data as the null distribution. Unable to plot both condience interval and envelope
simultaneously |
|
calculate_min_distance_to_borders()
|
calculate_min_distance_to_borders |
|
calculate_minimum_distances()
|
calculate_minimum_distances |
|
calculate_proportions_of_cells_in_structure()
|
calculate_proportions_of_cells_in_structure |
|
calculate_proportions_of_immune_cells_in_structure()
|
calculate_proportions_of_immune_cells_in_structure |
|
calculate_summary_distances_between_cell_types()
|
calculate_summary_distances_between_cell_types |
|
calculate_summary_distances_of_immune_cells_to_borders()
|
calculate_summary_distances_of_immune_cells_to_borders |
|
calculate_summary_distances_to_borders()
|
calculate_summary_distances_to_borders |
|
check_distribution_type()
|
check for initial underlying distribution (cluster or Homogenous Poisson) |
|
clusters_communities_morisita_index()
|
clusters_communities_morisita_index |
|
composition_of_clusters_and_communities()
|
composition_of_clusters_and_communities |
|
compute_mixing_score()
|
compute_mixing_score |
|
define_celltypes()
|
define_celltypes |
|
define_structure()
|
define_structure |
|
entropy()
|
entropy |
|
find_subset()
|
Determine point subset data |
|
fit_cluster_model()
|
Fit Cauchy model to point pattern |
|
fit_cluster_model_multiple_images()
|
Find and plot cluster model parameters of multiple images in a boxplot |
|
format_colData_to_sce()
|
format_colData_to_sce |
|
format_image_to_sce()
|
format_image_to_sce |
|
format_sce_to_ppp()
|
format_sce_to_ppp |
|
formatted_image
|
Example Inform image |
|
gradient()
|
gradient |
|
grid_metrics()
|
grid_metrics |
|
identify_bordering_cells()
|
identify_bordering_cells |
|
identify_bordering_cells2()
|
identify_bordering_cells |
|
identify_cell_clusters()
|
identify_cell_clusters |
|
identify_cell_communities()
|
identify_cell_communities |
|
image_splitter()
|
image_splitter |
|
marker_intensity_boxplot()
|
marker_intensity_boxplot |
|
marker_permutation()
|
marker_permutation |
|
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_multiple()
|
mixing_score_multiple |
|
mixing_score_summary()
|
mixing_score_summary |
|
morisita_index()
|
morisita_index |
|
number_of_cells_within_radius()
|
number_of_cells_within_radius |
|
plot_average_intensity()
|
plot_average_intensity |
|
plot_cell_basic()
|
plot_cell_basic |
|
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_proportions |
|
plot_composition_heatmap()
|
plot_composition_heatmap |
|
plot_distance_heatmap()
|
plot_distance_heatmap |
|
plot_marker_level_heatmap()
|
plot_marker_level_heatmap |
|
plot_mixing_score_summary()
|
plot_mixing_score_summary |
|
predict_phenotypes()
|
predict_phenotypes |
|
print_column()
|
print_column |
|
print_phenotypes()
|
print_phenotypes |
|
select_celltypes()
|
select_celltypes |
|
select_phenotypes()
|
select_phenotypes |