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,
  ...
)

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. Can be useful when analyses require comparisons between human and mouse gene names for example.
...	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)
}