As including a more detailed vignette inside the package makes the package exceed the tarball size, more detailed vignettes are hosted on an external website. This is a simplified vignette.
This package can be installed from Bioconductor:
if (!requireNamespace("BiocManager")) install.packages("BiocManager") BiocManager::install("Voyager") # Devel version # install.packages("remotes") remotes::install_github("pachterlab/Voyager")
In non-spatial scRNA-seq, the
SingleCellExperiment (SCE) package implements a data structure and other packages such as
scater implement methods for quality control (QC), basic exploratory data analysis (EDA), and plotting functions, using SCE to organize the data and results.
SpatialFeatureExperiment (SFE) aims to be analogous
scater to SFE, implementing basic exploratory spatial data analysis (ESDA) and plotting. SFE inherits from SCE and
SpatialExperiment (SPE), so all methods written for SCE and SPE can be used for SFE as well.
These are the main functionalities of the
Voyager at present:
colDataalong with annotation geometries, with colorblind friendly default palettes. The actual geometries are plotted, not just centroids as in
Seurat. The tissue image can be plotted behind the geometries.
Future versions may add user friendly wrappers of some successful spatial transcriptomics data analysis packages for spatially variable genes, cell type deconvolution, and spatial regions on CRAN, Bioconductor, pip, and conda, to provide a uniform syntax and avoid object conversion, as is done in
Seurat for some non-spatial scRNA-seq methods.
Here we use a mouse skeletal muscle Visium dataset from Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. It’s in the
SFEData package, as an SFE object, which contains Visium spot polygons, myofiber and nuclei segmentations, and myofiber and nuclei morphological metrics.
library(SFEData) library(SpatialFeatureExperiment) library(SpatialExperiment) library(ggplot2) library(Voyager) library(scater) library(scran) library(pheatmap)
This is the H&E image: