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Seurat
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, ... )
A Seurat object
Directory containing the H5 file specified by filename and the image data in a subdirectory called spatial
filename
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. Can be useful when analyses require comparisons between human and mouse gene names for example.
Name of image to pull the coordinates from
Arguments passed to Read10X_h5
Read10X_h5
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) }
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