Package index • Battlefield

All functions

add_borders_to_spe(): Add border or core spot selections to SpatialExperiment colData
add_layers_to_spe(): Add layer classifications to SpatialExperiment colData
add_trajectories_to_spe(): Add trajectory information to SpatialExperiment colData
adjacent_endpoint(): Pick a point adjacent to a selected endpoint, on a given side of a segment
bresenham_line(): Rasterize a line between two points using Bresenham's algorithm
build_all_borders(): Build border spots for all oriented cluster pairs
build_all_cores(): Build core spots for all oriented cluster pairs
build_one_line(): Build a single line of spots along a segment
build_one_trajectory(): Select spots near a segment and order them along the segment
build_similar_trajectories(): Build parallel spot lines around a central segment
closest_spot(): Find the closest spot to a target point
compute_centroids(): Compute cluster centroids (mean x/y per cluster)
count_all_inlaids(): Count inlaid composition for all clusters
count_all_neighborhoods(): Count neighborhood composition for all clusters
count_inlaid(): Count inlaid composition within a source cluster
count_neighborhood(): Count annotated spot types in the neighborhood of a cluster or point
create_all_layers(): Create and visualize layers for multiple clusters
create_cluster_layers(): Create layer classification for spots in a cluster
detect_grid_type(): Detect the grid type (square vs hexagonal) from spatial coordinates
directed_cluster_interface_pairs(): Build all oriented cluster pairs (A -> B) and their directed_pair labels
estimate_spot_spacing(): Estimate spot spacing from nearest-neighbor distances
filter_out_by_endpoint_clusters(): Filter lines by endpoint cluster membership
get_inlaid_spots(): Get inlaid spots within a source cluster
get_neighborhood_params(): Suggest neighborhood parameters based on detected grid type
get_neighborhood_spots(): Get neighborhood spots around a target cluster or point
point_segment_distance_vec(): Point-to-segment distance (vectorized)
remove_used_points(): Remove rows whose rounded (x, y) coordinates have already been used
select_border_spots(): Select border spots from cluster A that touch cluster B (and flag junctions)
select_core_spots(): Select core (non-interface) spots for a directed pair
shift_point(): Shift a point along a given direction vector
unit_normal_left(): Compute the left unit normal of the directed segment A->B
visiumHD_16um_simulated_spe: Simulated VisiumHD 16 µm binned SpatialExperiment dataset
visiumHD_simulated_spe: Simulated VisiumHD 8 µm binned SpatialExperiment dataset
visium_simulated_spe: Simulated Visium SpatialExperiment dataset