Load10X_Spatial | R Documentation |
Seurat
objectLoad 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,
...
)
data.dir |
Directory containing the H5 file specified by |
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 - 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 |
|
... |
Arguments passed to |
A Seurat
object
## 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)
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