Run Giotto spatial gene detection — RunGiottoSpatialGenes • scop

Use Giotto binSpect() as a temporary backend for spatially variable gene detection. The complete Giotto object and result tables are returned as a standalone result; the input Seurat object is not modified.

Usage

RunGiottoSpatialGenes(
  srt,
  assay = NULL,
  layer = "data",
  features = NULL,
  image = NULL,
  coord.cols = c("x", "y"),
  network_method = c("Delaunay", "kNN"),
  network_name = NULL,
  bin_method = c("kmeans", "rank"),
  set_variable_features = FALSE,
  top_n = 100,
  tool_name = "GiottoSpatialGenes",
  store_giotto = TRUE,
  conversion_params = list(),
  network_params = list(),
  binSpect_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 with Giotto::binSpect(). 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.
bin_method: Binarization method passed to Giotto::binSpect().
set_variable_features: Deprecated compatibility argument. Seurat variable features are never modified by this function.
top_n: Number of top genes to store.
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().
binSpect_params: Additional parameters passed to Giotto::binSpect().
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 gene table, top features, raw Giotto result, parameters, features, and cells.

Examples

data(visium_human_pancreas_sub)
spatial <- visium_human_pancreas_sub
spatial <- Seurat::NormalizeData(spatial, assay = "Spatial", verbose = FALSE)
giotto_genes <- list(
  results = data.frame(
    feat_ID = rownames(spatial)[1:6],
    spatGeneRank = c(40, 35, 28, 20, 16, 10)
  ),
  top_features = rownames(spatial)[1:4],
  parameters = list(assay = "Spatial", layer = "data", coord.cols = c("x", "y"))
)
class(giotto_genes) <- c("giotto2_spatial_genes", "giotto2_result", "list")

head(giotto_genes$results)
#>   feat_ID spatGeneRank
#> 1  TMSB4X           40
#> 2     UBC           35
#> 3     GCG           28
#> 4    ACTB           20
#> 5  COL3A1           16
#> 6  COL1A1           10
GiottoPlot(giotto_genes, plot_type = "ranking", top_n = 6)

GiottoPlot(
  giotto_genes,
  srt = spatial,
  plot_type = "feature",
  overlay_image = FALSE,
  coord.cols = c("x", "y")
)


if (
  isTRUE(check_r("giotto-suite/Giotto", verbose = FALSE))
) {
spatial <- Seurat::FindVariableFeatures(
  spatial,
  assay = "Spatial",
  nfeatures = 300,
  verbose = FALSE
)
giotto_genes <- RunGiottoSpatialGenes(
  spatial,
  assay = "Spatial",
  layer = "data",
  features = Seurat::VariableFeatures(spatial, assay = "Spatial"),
  coord.cols = c("x", "y"),
  top_n = 50
)
}
#> Error in check_r("giotto-suite/Giotto", verbose = FALSE): could not find function "check_r"