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pasta: Pattern Analysis for Spatial Omics daTA

This repository contains code for the pasta vignette accompanying the pasta preprint.

Disclaimer

This vignette should be a dynamic resource for people interested in spatial statistics for spatial omics data. The content is therefore subject to change. If you wish to contribute to this resource, feel free to open an issue or contact us via email.

Installing all necessary R packages

spatialFDA has to be installed via devtools::install_github("mjemons/spatialFDA") all other R packages can be installed using renv::restore().

Using renv and Python

It can happen that renv creates a virtual environment that does not locate the correct Python version and it will not be able to find the shared libraries.

To get a (hopefully) working environment:

  • Select your standart Python installation with renv::use_python(). It has to correspond to the Python version in the lock file (3.10.12).
  • This will create a virtual environment with the Python binary pointing to the selected version.
  • You can then use renv::restore to install both R and Python packages in the renv (virtual) environment.

Disclaimer: This was so far only tested on 3.10.12 | packaged by conda-forge and macOS Sonoma 14.7.1 - aarch64-apple-darwin20 (64-bit).

Contributions

Contributions are welcome. Please open an issue to start contributing.

License

© 2024 The pasta authors. Content is published under Creative Commons CC-BY-4.0 License for the text and GPL-3 License for any code.