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:
sfdata frame and the SFE object, which bring geospatial tools to spatial transcriptomics. A published Visium dataset already as an SFE object provided in the
SFEDatapackage is used for the demonstrations here and in part 3.
Voyagerpackage, 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.
SingleCellExperimentand preferably also
We 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.