Run BANKSY spatial clustering — RunBANKSY • scop

Build neighborhood-augmented BANKSY features from a spatial Seurat object and store spatial domain or microenvironment clusters in metadata.

Usage

RunBANKSY(
  srt,
  assay = NULL,
  layer = "data",
  features = NULL,
  image = NULL,
  coord.cols = c("col", "row"),
  lambda = 0.2,
  k_geom = 15,
  M = 1,
  npcs = 20,
  use_agf = FALSE,
  algo = "leiden",
  k_neighbors = 50,
  resolution = 0.6,
  group = NULL,
  seed = 1,
  compute_banksy_params = list(),
  run_pca_params = list(),
  cluster_banksy_params = list(),
  cluster_source = NULL,
  cluster_colname = "BANKSY_cluster",
  tool_name = "BANKSY",
  store_results = TRUE,
  verbose = TRUE
)

Arguments

srt: A Seurat object.
assay: Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.
layer: Assay layer used as BANKSY input.
features: Optional features to use. If NULL, all assay features are used after zero-count filtering.
image: Name of the Seurat spatial image used to recover spot coordinates when they are not already present in metadata. For regular Visium data with only pixel x/y coordinates, BayesSpace array coordinates are inferred from the spatial grid.
coord.cols: Metadata coordinate columns used when no image coordinate source is available.
lambda: BANKSY spatial weighting parameter.
k_geom: Number of spatial neighbors used by BANKSY.
M: Highest azimuthal Fourier harmonic passed to BANKSY.
npcs: Number of principal components to compute.
use_agf: Whether to use azimuthal Gabor filters.
algo: Clustering algorithm passed to Banksy::clusterBanksy().
k_neighbors: Number of neighbors for graph clustering.
resolution: Graph clustering resolution.
group: Optional metadata column used by BANKSY for multi-sample scaling. It is copied into the SpatialExperiment colData.
seed: Optional seed for PCA and clustering.
compute_banksy_params: Additional parameters passed to Banksy::computeBanksy().
run_pca_params: Additional parameters passed to Banksy::runBanksyPCA().
cluster_banksy_params: Additional parameters passed to Banksy::clusterBanksy().
cluster_source: Optional BANKSY colData column to copy. If NULL, the first cluster name reported by Banksy::clusterNames() is used when available.
cluster_colname: Metadata column used for BANKSY clusters.
tool_name: Name used to store detailed results in srt@tools.
store_results: Whether to store detailed BANKSY results in srt@tools.
verbose: Whether to print the message. Default is TRUE.

Value

A Seurat object with BANKSY clusters in metadata. When store_results = TRUE, detailed results are stored in srt@tools[[tool_name]].

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial$BANKSY_cluster <- factor(
  paste0("BANKSY", (seq_len(ncol(spatial)) - 1) %% 3 + 1)
)

SpatialSpotPlot(
  spatial,
  group.by = "BANKSY_cluster",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)


if (
  requireNamespace("Banksy", quietly = TRUE)
) {
spatial <- RunBANKSY(
  spatial,
  assay = "Spatial",
  layer = "counts",
  coord.cols = c("x", "y"),
  features = rownames(spatial)[1:300],
  lambda = 0.2,
  k_geom = 8,
  resolution = 0.6,
  verbose = FALSE
)
}
#> Computing neighbors...
#> Spatial mode is kNN_median
#> Parameters: k_geom=8
#> Done
#> Computing neighbors...
#> Spatial mode is kNN_median
#> Parameters: k_geom=8
#> Done
#> Done
#> Centering
#> Done
#> Using seed=1
#> Using seed=1