Load10X_Spatial: Load a 10x Genomics Visium Spatial Experiment into a 'Seurat'...
In ibseq/scs-analysis: Tools for Single Cell Genomics

Description Usage Arguments Value Examples

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,
  ...
)

`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`

A Seurat object

## Not run: 
data_dir <- 'path/to/data/directory'
list.files(data_dir) # Should show filtered_feature_bc_matrix.h5
Load10X_Spatial(data.dir = data_dir)

## End(Not run)