Introduction

SpatialData.data package provides utilities for accessing, reading and generating SpatialData datasets. Data from a variety of spatial omics technologies has been made available as SpatialData (zipped) .zarr stores.

These scverse SpatialData examples are available through sources

1. biocOSN: Bioc’s NSF OSN bucket,
2. biocOSN_Xenium: Bioc’s NSF OSN bucket for raw data outputs from some Xenium datasets and
3. sandbox: scverse’s spatialdata-sandbox (https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html)

SpatialData.data uses basilisk to interface and maintain multiple versions of scverse’s spatialdata module (0.5 and 0.8) for reading and writing to .zarr stores.

The package also incorporates dummy-spatialdata python module that generates toy SpatialData examples whose elements are customized by the user. These examples can be generated again using spatialdata module versions 0.5 and 0.8.

Please visit the vignette for more information.

Installation

if(!requireNamespace("BiocManager"))
  install.packages("BiocManager")
BiocManager::install("spatialdataR")
BiocManager::install("SpatialData.data")

library(spatialdataR)
#> 
#> Attaching package: 'spatialdataR'
#> The following object is masked from 'package:stats':
#> 
#>     filter
library(SpatialData.data)

To interrogate our S3 bucket you will need paws.storage installed.

if(!requireNamespace("paws.storage"))
  install.packages("paws.storage")
library(paws.storage)
Sys.setenv(AWS_REGION = "us-east-1") 

Load SpatialData (.zarr) from Archives

Any spatialdata dataset can be retrieved (once) into some location, and read into R.

(x <- SD.data_load("ColorectalCarcinomaMIBITOF"))
#> checking Bioconductor OSN bucket...
#> class: SpatialData
#> - images(3):
#>   - point16_image (3,1024,1024)
#>   - point23_image (3,1024,1024)
#>   - point8_image (3,1024,1024)
#> - labels(3):
#>   - point16_labels (1024,1024)
#>   - point23_labels (1024,1024)
#>   - point8_labels (1024,1024)
#> - points(0):
#> - shapes(0):
#> - tables(1):
#>   - table (36,3309) [point8_labels,point16_labels,point23_labels]
#> coordinate systems(3):
#> - point16(2): point16_image point16_labels
#> - point23(2): point23_image point23_labels
#> - point8(2): point8_image point8_labels

You can view a list of available datasets using:

SD.data_list()
#>  [1] "MouseIntestineVisHD"        "MouseBrainVisHD"           
#>  [3] "MouseBrainVis"              "LungAdenocarcinomaMCMICRO" 
#>  [5] "MouseBrainMERFISH"          "MouseLiverMERFISH"         
#>  [7] "ColorectalCarcinomaMIBITOF" "MulticancerSteinbock"      
#>  [9] "JanesickBreastVisiumEnh"    "JanesickBreastXeniumRep1"  
#> [11] "JanesickBreastXeniumRep2"   "HumanLungMulti_10x"        
#> [13] "Breast2fov_10x"             "Lung2fov_10x"              
#> [15] "SpaceMHelaniH3T3"