Package index • tessera

All functions

AddAggsAdjacencyMatrix(): Construct tile adjacency matrix from consolidated GetTiles output.
ConsolidateResults(): Consolidate Tessera results from multiple samples (groups) after constructing Tessera tiles separately on cells from each group.
GetTiles(): Generic function that runs the Tessera algorithm on single-cell spatial data
GetTiles(<Seurat>): Applies Tessera on a Seurat object
GetTiles(<default>): Run full DMT segmentation pipeline to make aggregated tiles from cells
RunUMAPCustom(): Run UMAP and save fgraph and embeddings in Seurat object
add_exterior_triangles(): For every edge on the boundary, adds a second degenerate triangle
assign_unique_rowid_cpp(): Assigns a unique ID to each point with distinct X,Y coordinates
compress_field_cpp(): Compress a gradient field using SVD
compress_gradients_svd(): Compress a gradient field using SVD
compute_gradients(): Compute spatial gradient field for input to DMT
compute_gradients_edges(): Compute spatial gradient field for input to DMT
dmt_assign_tiles(): Assign points to tiles after DMT
dmt_get_separatrices(): Get separatrices that separate points into components with strong boundaries
dmt_init_tiles(): Initialize tiles with shapes and other properties
dmt_set_f(): Set DMT scalar field values as the Frobenius norm of the total derivative
do_dmt_forest_cpp(): Construct maximum spanning forest
do_dual_forest(): Construct dual maximum spanning forest on triangles
do_pca(): Compute PCA embeddings from a raw counts matrix
do_primary_forest(): Construct primal minimum spanning forest on points
estimate_field(): Compute a spatial gradient field at each point (cell)
estimate_field_cpp(): Compute a spatial gradient field at each point (cell)
estimate_field_edges_cpp(): Compute a spatial gradient field along each edge
findDuplicates(): Find duplicates within a vector
get_e_sep(): Get the collection of edges that lie along separatrices
init_data(): Generate mesh data structure from coordinates, for input to DMT analysis
init_edges_cpp(): Calculates triangles' centroids, areas, and heights from vertices
init_scores(): Initialize tile scores for aggregation
init_tris_cpp(): Calculates triangles' centroids, areas, and heights from vertices
inv_svd_field_cpp(): Inverse SVD transform to reconstruct spatial gradient field
mergeListsToArmaUVec(): Copies elements from two lists an Armadillo uvec
merge_aggs(): Merges tiles using single-linkage agglomerative clustering
merge_aggs_cpp(): Merges tiles using single-linkage agglomerative clustering
normalize_data(): Log-normalization for counts data
procrustes_inner(): Computes the procrustes inner product between two matrices
procrustes_mat(): Solves the orthogonal procrustes problem
prune_graph(): Prunes mesh by eliminating long edges and small connected components
scaleRows_dgc(): Z-score a sparse matrix across each row
scale_data(): Z-score a sparse matrix across each row or column
smooth_embedding(): Smooth embeddings along edges
smooth_field(): Bilateral / anisotropic filtering of gradient field
smooth_field_cpp(): Bilateral / anisotropic filtering of gradient field
smooth_field_edges(): Bilateral / anisotropic filtering of gradient field
smooth_field_edges_cpp(): Bilateral / anisotropic filtering of gradient field
svd_field_cpp(): Compute the SVD of a spatial gradient field at each point (or edge/triangle)
tessera-package tessera: Accurate tiling of spatial single-cell data
tessera_warmup: Sample data for Tessera vignettes
trace_back_cpp(): Trace back from a point to its root in the spanning forest
trace_epaths_cpp(): Trace all paths from saddles to critical points in the spanning forest
trace_paths(): Trace all paths from saddles to dual critical points in the spanning forest.
trace_polygons(): Contruct shapes that outline each tile
trace_polygons_cpp(): Contruct shapes that outline each tile
update_E_cpp(): Updates information for boundaries after merging two tiles
update_V_cpp(): Updates information for tiles after merging two tiles
update_agg_shapes(): Update shapes and counts matrix for tiles after merging
update_dmt_aggid(): Update tile IDs in the DMT data structure after merging