Seurat (version 4.3.0.1)

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",
  filter.matrix = TRUE,
  to.upper = FALSE,
  image = NULL,
  ...
)

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

filter.matrix

Only keep spots that have been determined to be over tissue

to.upper

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.

image

An object of class VisiumV1. Typically, an output from Read10X_Image

...

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)
}