Here we demonstrate the SpatialFeatureExperiment
(SFE), an S4 class that brings Simple Features (as in the sf
package) to SpatialExperiment
, and exploratory spatial data analysis (ESDA) with the SFE object with the Voyager
package. This workshop has 3 parts:
sf
data frame and the SFE object, which bring geospatial tools to spatial transcriptomics. A published Visium dataset already as an SFE object provided in the SFEData
package is used for the demonstrations here and in part 3.Voyager
package, applying geospatial tools on the SFE object. The ESDA includes computing Moran’s I and Geary’s C for spatial autocorrelation, permutation testing for Moran’s I, correlograms, and Moran scatter plot.SingleCellExperiment
and preferably also SpatialExperiment
classessf
is preferableWe have submitted the packages presented in this workshop to Bioconductor. Before they get accepted, they can be installed from GitHub:
devtools::install_github("pachterlab/SFEData")
devtools::install_github("pachterlab/SpatialFeatureExperiment")
devtools::install_github("pachterlab/Voyager")
docker run -e PASSWORD=abc -p 8787:8787 ghcr.io/lambdamoses/sfeworkshop:latest
Once running, navigate to http://localhost:8787/ and then login with username rstudio and password abc.