Export data for FeatureViewer
ExportDataForViewer.Rd
This is a utility function used to export data required for FeatureViewer
.
Usage
ExportDataForViewer(
object,
sampleIDs = NULL,
outdir,
nCores = detectCores() - 1,
overwrite = FALSE,
verbose = TRUE
)
Arguments
- object
A
Seurat
object created withsemla
- sampleIDs
An integer vector specifying the sampleIDs for the datasets to export. By default, all samples are exported.
- outdir
A character vector specifying the path to an existing directory with permission to read and write files.
- nCores
Number of cores to use parallel image tiling
- overwrite
Overwrite files if they already exists
- verbose
Print messages
Details
FeatureViewer
will automatically attempt to export these files every time it's run.
With ExportDataForViewer
, you only have to export the files once and you can provide the output
data path for FeatureViewer
to look for the required files in that directory.
See also
Other feature-viewer-methods:
FeatureViewer()
Examples
library(semla)
se_mbrain <- readRDS(system.file("extdata/mousebrain",
"se_mbrain",
package = "semla"))
se_mbrain <- LoadImages(se_mbrain)
#>
#> ── Loading H&E images ──
#>
#> ℹ Loading image from /private/var/folders/8r/bfm2m_q17znfk0m_8dt330tm0000gp/T/RtmpLHpYU7/temp_libpath305b1609463d/semla/extdata/mousebrain/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 600x565 to 400x377 pixels
#> ℹ Saving loaded H&E images as 'rasters' in Seurat object
# Export viewer files to a temporary directory
outpath <- ExportDataForViewer(se_mbrain, outdir = tempdir(), nCores = 1, overwrite = TRUE)
#> ℹ Attempting to tile H&E image(s)
#> ℹ Got an image of dimensions 600x565 for sample 1
#> → Tiling image into 2 zoom levels
#> → Creating tiles
#> → Exporting tiles
#> → Exporting meta data
#> → Exporting Visium coordinates
outpath
#> [1] "/private/var/folders/8r/bfm2m_q17znfk0m_8dt330tm0000gp/T/RtmpRVvGCP/viewer_data"