Seurat
objectR/preprocessing.R
Load10X_Spatial.Rd
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",
bin.size = NULL,
filter.matrix = TRUE,
to.upper = FALSE,
image = NULL,
...
)
Directory containing the H5 file specified by filename
and the image data in a subdirectory called spatial
Name of H5 file containing the feature barcode matrix
Name of the initial assay
Name for the stored image of the tissue slice
Specifies the bin sizes to read in - defaults to c(16, 8)
Only keep spots that have been determined to be over tissue
Converts all feature names to upper case. Can be useful when analyses require comparisons between human and mouse gene names for example.
VisiumV1
/VisiumV2
instance(s) - if a vector is
passed in it should be co-indexed with `bin.size`
Arguments passed to Read10X_h5
A Seurat
object
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)
}