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Installation

Source: vignettes/articles/Install.Rmd
Install.Rmd

Install STcompare

STcompare depends on Bioconductor packages (SpatialExperiment, SEraster and others). Install it with BiocManager, which finds them; BiocManager uses the remotes package to install packages from GitHub:

install.packages(c("BiocManager", "remotes"))
BiocManager::install("JEFworks-Lab/STcompare")

STcompare needs R 4.5 or later: SEraster is distributed by Bioconductor from release 3.21, which requires R 4.5.

A C++17 compiler

STcompare contains compiled code, so installing it from source needs a C++17 compiler:

  • macOS: the Xcode command line tools. Run xcode-select --install in a terminal.
  • Windows: Rtools, the version that matches your version of R.
  • Linux: the C++ compiler of your distribution, for example sudo apt install build-essential on Debian and Ubuntu. SEraster also needs the system libraries of the sf package (GDAL, GEOS and PROJ); see the sf installation notes.

The compiled code reproduces R’s arithmetic exactly, so the installation stops with an explanatory error if the compiler flags include -ffast-math, -Ofast or similar options, for example from ~/.R/Makevars. Remove them and install again.

Check the installation 

library(STcompare)
example(compareSpatial)

The example rasterizes the simulated kidneys that ship with the package and compares them in a few seconds.

compareSpatial() runs its permutations on several threads. Set the number once per session, for example to 8:

options(STcompare.nThreads = 8)

The legacy correlation functions, such as spatialCorrelationGeneExp(), do not read this option; give them the number of threads with their argument nThreads.

The first use of the Bioconductor packages in a session can print lines such as Warning: stack imbalance in '<-', 2 then 3. They come from a dependency (SparseArray) when its namespace is loaded and are harmless.

Packages for the tutorials

The tutorials use a few more packages: patchwork to arrange the figures, rhdf5 to read the 10x HDF5 files of the kidney case study, and jsonlite for the brain case study.

BiocManager::install(c("patchwork", "rhdf5", "jsonlite"))

To install the vignettes with the package, so that browseVignettes("STcompare") lists them, also install the packages that build them (knitr and rmarkdown, among the suggested packages):

BiocManager::install("JEFworks-Lab/STcompare", build_vignettes = TRUE,
                     dependencies = TRUE)