Load a 10x Genomics Visium Spatial Experiment into a Seurat object

Load a 10x Genomics Visium Spatial Experiment into a Seurat object

Load10X_Spatial(
  data.dir,
  filename = "filtered_feature_bc_matrix.h5",
  assay = "Spatial",
  slice = "slice1",
  filter.matrix = TRUE,
  to.upper = FALSE,
  image = NULL,
  ...
)

Arguments

data.dir: Directory containing the H5 file specified by filename and the image data in a subdirectory called spatial
filename: Name of H5 file containing the feature barcode matrix
assay: Name of the initial assay
slice: Name for the stored image of the tissue slice
filter.matrix: Only keep spots that have been determined to be over tissue
to.upper: Converts all feature names to upper case. This can provide an approximate conversion of mouse to human gene names which can be useful in an explorative analysis. For cross-species comparisons, orthologous genes should be identified across species and used instead.
image: An object of class VisiumV1. Typically, an output from Read10X_Image
...: Arguments passed to Read10X_h5

Value

A Seurat object

Examples

if (FALSE) {
data_dir <- 'path/to/data/directory'
list.files(data_dir) # Should show filtered_feature_bc_matrix.h5
Load10X_Spatial(data.dir = data_dir)
}