Seurat: Load10X_Spatial – R documentation

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Seurat

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,
  ...
)

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. Can be useful when analyses require comparisons between human and mouse gene names for example.
`...`	Arguments passed to `Read10X_h5`

Value

A Seurat object

Examples

## Not run: 
data_dir <- 'path/to/data/directory'
list.files(data_dir) # Should show filtered_feature_bc_matrix.h5
Load10X_Spatial(data.dir = data_dir)

## End(Not run)

Seurat

Tools for Single Cell Genomics

v4.0.1

GPL-3 | file LICENSE

Authors

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17

Load10X_Spatial

Description

Usage

Arguments

Value

Examples

Seurat

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