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",
  bin.size = NULL,
  filter.matrix = TRUE,
  to.upper = FALSE,
  image = NULL,
  image.name = "tissue_lowres_image.png",
  segmentation.type = NULL,
  compact = TRUE,
  ...
)

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
bin.size: Specifies the bin sizes to read in, can include "polygons" to load segmentations. Defaults to c(16, 8)
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.
image: VisiumV1/VisiumV2 instance(s) - if a vector is passed in it should be co-indexed with `bin.size`
image.name: Name of the tissue image to be plotted. Defaults to tissue_lowres_image.png
segmentation.type: Which segmentations to load (cell or nucleus) when bin.size includes "polygons". Defaults to "cell".
compact: Whether to store segmentations in only the sf.data slot in the corresponding Segmentation object (default TRUE) to save memory and processing time. If FALSE, segmentations are also stored in sp format in addition to the sf.data slot.
...: 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)
}