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README.md
# Save `SpatialExperiment`s to file |Environment|Status| |---|---| |[BioC-release](https://bioconductor.org/packages/release/bioc/html/alabaster.spatial.html)|[![Release OK](https://bioconductor.org/shields/build/release/bioc/alabaster.spatial.svg)](http://bioconductor.org/checkResults/release/bioc-LATEST/alabaster.spatial/)| |[BioC-devel](https://bioconductor.org/packages/devel/bioc/html/alabaster.spatial.html)|[![Devel OK](https://bioconductor.org/shields/build/devel/bioc/alabaster.spatial.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/alabaster.spatial/)| 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](https://bioconductor.org/packages/alabaster.spatial): ```r # install.packages("BiocManager") BiocManager::install("alabaster.spatial") ``` In the example below, we save a `SpatialExperiment` object to file: ```r 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" ```