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",
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
Only keep spots that have been determined to be over tissue
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.
An object of class VisiumV1. Typically, an output from Read10X_Image
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)
}