Applies Tessera on a Seurat object

Usage

# S3 method for class 'Seurat'
GetTiles(
  obj,
  spatial,
  embeddings = NULL,
  dims.use = NULL,
  assay = NULL,
  group.by = NULL,
  raw_results = FALSE,
  tile.id.name = "tile_id",
  reduction.name = "pca",
  graph.name = "tile_adj",
  add.isolated.cells = TRUE,
  ...
)

Arguments

obj

Seurat object with spatial coordinates (and optionally, pre-computed single cell embeddings) stored as dimensional reductions.

spatial

Name of dimensional reduction where the cells' x/y coordinates are stored.

embeddings

Name of dimensional reduction where pre-computed single-cell embeddings are stored (a num_cells x num_dim matrix of cell embeddings across all latent dimensions). If missing, cell embeddings are calculated using PCA. If provided, the npcs parameter is ignored.

assay

Seurat assay to pull data for when using the cell counts. Defaults to the DefaultAssay.

group.by

Name of column in obj@meta.data to use for grouping cells into separate samples.

raw_results

Whether to return the raw results from GetTiles.default().

tile.id.name

Name of variable to store the tile IDs in the cell-level Seurat object.

reduction.name

Name of dimensional reduction to store the aggregated tile-level embeddings in the tile-level Seurat object.

graph.name

Name of graph to store tile adjacency matrix in the tile-level Seurat object.

add.isolated.cells

Whether to add back isolated single cells that were pruned out. Only applies when embeddings are provided. Defaults to TRUE.

...

Arguments passed on to GetTiles.default

meta_vars_include: Names of columns in meta_data to include in dmt$pts.
npcs: Number of PCs to compute for input to segmentation. Ignored if embeddings are provided directly.
smooth_emb: Number of smoothing iterations to perform on the cell embeddings prior to gradient computation. If a vector, then embeddings after each specified iteration are concatenated. If 0 is included, then the original embeddings are also included.
prune_thresh_quantile: Floating point value between 0 and 1, inclusive. Quantile of edge length above which edges are pruned. Defaults to 0.95.
prune_min_cells: Minimum number of cells required for a connected component of triangles to be kept. Defaults to 10.
prune_thresh: Edge length above which edges are pruned. If equal to NA, then this value is ignored and thresh_quantile is used to compute the threshold. Otherwise, if thresh is set, then thresh_quantile is ignored. Defaults to NA.
smooth_distance: One of c('none', 'euclidean', 'projected', 'constant'). If either smooth_distance or smooth_similarity is 'none', then no smoothing of the gradient field is conducted. Defaults to 'projected'.
smooth_similarity: One of c('none', 'euclidean', 'projected', 'constant'). If either smooth_distance or smooth_similarity is 'none', then no smoothing of the gradient field is conducted. Defaults to 'projected'.
smooth_iter: Number of rounds of gradient smoothing.
max_npts: Maximum number of cells allowed in each tile during the agglomerative clustering phase.
min_npts: Minimum number of cells allowed in each tile during the agglomerative clustering phase.
alpha: Parameter for scoring transcriptional similarity between adjacent tiles during the agglomerative clustering phase. For alpha, 0.2 = conservative merging, 2 = liberal merging.
future.globals.maxSize: Maximum allowed size (in bytes) of global variables that are exported to each parallel worker. Increase this value if you get an error about global object size. Default is 8*1024^3 (8 GB).
consolidate: Whether to consolidate results from multiple groups into a single collection of points and tiles (TRUE) or to return a list of separate results for each group (FALSE).
verbose: Whether to print progress messages for each stage of the segmentation pipeline.

Value

A List containing a pair of Seurat objects:

obj: the input single-cell object whose meta.data has been updated with tile assignments for each cell
tile_obj: a Seurat object where each item represents an individual Tessera tile

Applies Tessera on a Seurat object

Usage

Arguments

Value

See also