Run Giotto spatial co-expression modules — RunGiottoSpatialModules • scop

Use Giotto detectSpatialCorFeats() and clusterSpatialCorFeats() as a temporary backend for feature-level spatial co-expression modules. The complete Giotto object and module results are returned as a standalone result; the input Seurat object is not modified.

Usage

RunGiottoSpatialModules(
  srt,
  assay = NULL,
  layer = "data",
  features = NULL,
  image = NULL,
  coord.cols = c("x", "y"),
  network_method = c("Delaunay", "kNN"),
  network_name = NULL,
  cor_method = c("pearson", "spearman", "kendall"),
  k = 10,
  tool_name = "GiottoSpatialModules",
  store_giotto = TRUE,
  conversion_params = list(),
  network_params = list(),
  detect_params = list(),
  cluster_params = list(),
  verbose = TRUE,
  seed = 11
)

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 the expression matrix.
features: Features to test for spatial co-expression modules. If NULL, current variable features are used, falling back to all assay features.
image: Name of the Seurat spatial image used by the spatial workflow. If NULL, the first image is used when present.
coord.cols: Metadata coordinate columns used by the spatial workflow when no image is available.
network_method: Spatial network method passed to Giotto::createSpatialNetwork().
network_name: Name for the Giotto spatial network.
cor_method: Correlation method used by Giotto.
k: Number of feature modules passed to Giotto clustering.
tool_name: Result name recorded in returned parameters. This function does not write to srt@tools.
store_giotto: Deprecated compatibility argument. The complete Giotto object is always returned in the giotto element.
conversion_params: Additional parameters passed to Giotto::createGiottoObject().
network_params: Additional parameters passed to Giotto::createSpatialNetwork().
detect_params: Additional parameters passed to Giotto::detectSpatialCorFeats().
cluster_params: Additional parameters passed to Giotto::clusterSpatialCorFeats().
verbose: Whether to print the message. Default is TRUE.
seed: Random seed for reproducibility. Default is 11.

Value

A giotto2_result list containing the full Giotto object, spatial correlation object, module object, extracted module tables, parameters, features, and cells.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
module_features <- rownames(spatial)[1:4]
module_cor <- expand.grid(
  feat_ID = module_features,
  variable = module_features
)
module_cor$spat_cor <- c(
  1, 0.4, 0.1, -0.2,
  0.4, 1, 0.3, 0.0,
  0.1, 0.3, 1, 0.5,
  -0.2, 0.0, 0.5, 1
)
giotto_modules <- list(
  module_tables = list(result.cor_DT = module_cor),
  features = module_features,
  parameters = list(assay = "Spatial", layer = "data")
)
class(giotto_modules) <- c("giotto2_spatial_modules", "giotto2_result", "list")

names(giotto_modules$module_tables)
#> [1] "result.cor_DT"
GiottoPlot(giotto_modules, top_n = 4)


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)
spatial <- Seurat::FindVariableFeatures(
  spatial,
  assay = "Spatial",
  nfeatures = 300,
  verbose = FALSE
)
giotto_modules <- RunGiottoSpatialModules(
  spatial,
  assay = "Spatial",
  layer = "data",
  features = Seurat::VariableFeatures(spatial, assay = "Spatial")[1:50],
  coord.cols = c("x", "y"),
  cor_method = "pearson",
  k = 6
)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"