# Swiss-army toolkit for selecting niche fronts and invasive margins in spatial transcriptomics data

## Documentation for package ‘Battlefield’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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_8um_simulated_spe | Simulated VisiumHD 8 µm binned SpatialExperiment dataset
visium_simulated_spe | Simulated Visium SpatialExperiment dataset