| Environment | Status |
|---|---|
| BioC-release |  |
| BioC-devel |  |
The alabaster.spatial package implements methods for saving and loading SpatialExperiment objects under the alabaster framework.
This includes the spatial coordinates and images associated with each sample.
To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.spatial")In the example below, we save a SpatialExperiment object to file:
library(SpatialExperiment)
example(SpatialExperiment, echo=FALSE) # can't be bothered to copy it here.
spe
## class: SpatialExperiment
## dim: 50 99
## metadata(0):
## assays(1): counts
## rownames(50): ENSMUSG00000051951 ENSMUSG00000089699 ...
## ENSMUSG00000005886 ENSMUSG00000101476
## rowData names(1): symbol
## colnames(99): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
## AAAGTCGACCCTCAGT-1 AAAGTGCCATCAATTA-1
## colData names(4): in_tissue array_row array_col sample_id
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
## imgData names(4): sample_id image_id data scaleFactor
library(alabaster.spatial)
tmp <- tempfile()
saveObject(spe, tmp)
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "SpatialExperiment"
## attr(,"package")
## [1] "SpatialExperiment"