Seurat (version 5.4.0)

Load10X_Spatial: Load a 10x Genomics Visium Spatial Experiment into a Seurat object

Description

Load a 10x Genomics Visium Spatial Experiment into a Seurat object

Usage

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,
  ...
)

Value

A Seurat object

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

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)
}