This repository contains code to reproduce analysis and figures of the pasta preprint.
R packages are managed with renv. To install R packages you can use renv::restore().
We use public datasets for all plots. The STARmap dataset used in figure 1 can be downloaded from the singe cell portal as specified in the Bansky vignette. All other datasets are downloaded when running code/utils.R.
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] stringr_1.5.1 SFEData_1.10.0 scales_1.4.0
[4] tmap_4.1 scater_1.36.0 scuttle_1.18.0
[7] RColorBrewer_1.1-3 viridis_0.6.5 viridisLite_0.4.2
[10] ggspavis_1.14.3 imcdatasets_1.16.0 cytomapper_1.20.0
[13] EBImage_4.50.0 sosta_1.0.1 ggrastr_1.0.2
[16] STexampleData_1.16.0 ExperimentHub_2.16.1 AnnotationHub_3.16.1
[19] BiocFileCache_2.16.1 dbplyr_2.5.0 patchwork_1.3.1
[22] SpaNorm_1.2.0 pals_1.10 SpatialExperiment_1.18.1
[25] SingleCellExperiment_1.30.1 SummarizedExperiment_1.38.1 Biobase_2.68.0
[28] GenomicRanges_1.60.0 GenomeInfoDb_1.44.1 IRanges_2.42.0
[31] S4Vectors_0.46.0 BiocGenerics_0.54.0 generics_0.1.4
[34] MatrixGenerics_1.20.0 matrixStats_1.5.0 BiocParallel_1.42.1
[37] spatialFDA_1.0.0 openxlsx_4.2.8 spatstat_3.4-0
[40] spatstat.linnet_3.3-1 spatstat.model_3.4-0 rpart_4.1.24
[43] spatstat.explore_3.5-2 nlme_3.1-168 spatstat.random_3.4-1
[46] spatstat.geom_3.5-0 spatstat.univar_3.1-4 spatstat.data_3.1-6
[49] Voyager_1.9.2 SpatialFeatureExperiment_1.10.1 ggplot2_3.5.2
[52] tidyr_1.3.1 spdep_1.3-13 sf_1.0-21
[55] spData_2.3.4 dplyr_1.1.4