spatialDE

The spatialDE package provides an R wrapper for the Python SpatialDE library, using reticulate and basilisk.

SpatialDE, by Svensson et al., 2018, is a method to identify spatially variable genes (SVGs) in spatially resolved transcriptomics data.

This package started as part of the BiocSpatialChallenges.

Installation instructions

The development version of spatialDE can be installed from GitHub with:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
    
BiocManager::install("sales-lab/spatialDE")

Basic usage

library(spatialDE)
spe <- mockSVG(return_SPE = TRUE)
de_results <- spatialDE(spe)
head(de_results)
#>            FSV M         g   l    max_delta      max_ll max_mu_hat max_s2_t_hat
#> 0 6.893971e-01 4 Gene_0001 0.5 4.480494e-01 -12.5057349  -44.97443 1.016237e+03
#> 1 2.049747e-09 4 Gene_0002 0.5 4.851652e+08 -23.3349972  -25.89877 1.382703e-06
#> 2 2.049747e-09 4 Gene_0003 0.5 4.851652e+08  -3.8319606  -47.30915 4.613312e-06
#> 3 2.049747e-09 4 Gene_0004 0.5 4.851652e+08  -0.8721812  -51.75744 5.521607e-06
#> 4 2.049747e-09 4 Gene_0006 0.5 4.851652e+08 -22.7027842  -22.22222 1.018043e-06
#> 5 2.049747e-09 4 Gene_0008 0.5 4.851652e+08  -1.4240589  -43.55167 3.909613e-06
#>   model   n     s2_FSV  s2_logdelta        time      BIC max_ll_null
#> 0    SE 100  4.1604136 9.981394e+01 0.001912832 43.43215  -13.070591
#> 1    SE 100  0.6775166 1.167603e+17 0.003101826 65.09068  -23.337514
#> 2    SE 100  0.1014734 1.748749e+16 0.003578186 26.08460   -3.834477
#> 3    SE 100  2.1406586 3.689118e+17 0.003778219 20.16504   -0.874698
#> 4    SE 100 11.2472218 1.938297e+18 0.002474070 63.82625  -22.705301
#> 5    SE 100  0.4912790 8.466489e+16 0.004010916 21.26880   -1.426576
#>           LLR      pval      qval
#> 0 0.564856105 0.4523102 0.9599889
#> 1 0.002516790 0.9599888 0.9599889
#> 2 0.002516786 0.9599888 0.9599889
#> 3 0.002516791 0.9599888 0.9599889
#> 4 0.002516792 0.9599888 0.9599889
#> 5 0.002516790 0.9599888 0.9599889

Citation

Below is the citation output from using citation('spatialDE') in R. Please run this yourself to check for any updates on how to cite spatialDE.

Please note that this package merely provides a wrapper to use the original Python methods in R. If you find these methods useful, please also consider citing the original paper.

  Davide Corso and Milan Malfait (2021). spatialDE: R wrapper for
  SpatialDE. R package version 0.2.0.
  https://github.com/sales-lab/spatialDE

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {spatialDE: R wrapper for SpatialDE},
    author = {Davide Corso and Milan Malfait},
    year = {2021},
    note = {R package version 0.2.0},
    url = {https://github.com/sales-lab/spatialDE},
  }

Svensson V, Teichmann SA, Stegle O (2018). "SpatialDE: identification
of spatially variable genes." _Nature Methods_, *15*(5), 343-346. ISSN
1548-7105, doi: 10.1038/nmeth.4636 (URL:
https://doi.org/10.1038/nmeth.4636), <URL:
https://www.nature.com/articles/nmeth.4636>.

A BibTeX entry for LaTeX users is

  @Article{,
    title = {SpatialDE: identification of spatially variable genes},
    author = {Valentine Svensson and Sarah A. Teichmann and Oliver Stegle},
    copyright = {2018 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
    year = {2018},
    journal = {Nature Methods},
    volume = {15},
    pages = {343--346},
    number = {5},
    doi = {10.1038/nmeth.4636},
    issn = {1548-7105},
    url = {https://www.nature.com/articles/nmeth.4636},
  }

Code of Conduct

Please note that the spatialDE project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Useful links