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)
}