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().
spatialFDAhas to be installed viadevtools::install_github("mjemons/spatialFDA").sostahas to be installed viadevtools::install_github("sgunz/sosta").
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 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.7.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
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] data.table_1.16.4 Banksy_1.0.0 imcdatasets_1.12.0
[4] cytomapper_1.16.0 sosta_0.99.1 scales_1.3.0
[7] tidyr_1.3.1 RColorBrewer_1.1-3 viridis_0.6.5
[10] viridisLite_0.4.2 ggspavis_1.10.0 spatialFDA_0.99.1
[13] MerfishData_1.6.0 EBImage_4.46.0 magrittr_2.0.3
[16] stringr_1.5.1 dixon_0.0-9 splancs_2.01-45
[19] sp_2.1-4 spdep_1.3-8 spData_2.3.3
[22] tmap_3.3-4 scater_1.32.1 scran_1.32.0
[25] scuttle_1.14.0 SFEData_1.6.0 Voyager_1.6.0
[28] SpatialFeatureExperiment_1.6.1 ncf_1.3-2 sf_1.0-19
[31] reshape2_1.4.4 patchwork_1.3.0 STexampleData_1.12.3
[34] ExperimentHub_2.12.0 AnnotationHub_3.12.0 BiocFileCache_2.12.0
[37] dbplyr_2.5.0 RANN_2.6.2 rlang_1.1.4
[40] ggplot2_3.5.1 dplyr_1.1.4 mixR_0.2.1
[43] spatstat_3.3-0 spatstat.linnet_3.2-3 spatstat.model_3.3-3
[46] rpart_4.1.23 spatstat.explore_3.3-3 nlme_3.1-166
[49] spatstat.random_3.3-2 spatstat.geom_3.3-4 spatstat.univar_3.1-1
[52] spatstat.data_3.1-4 SpatialExperiment_1.14.0 SingleCellExperiment_1.26.0
[55] SummarizedExperiment_1.34.0 Biobase_2.64.0 GenomicRanges_1.56.2
[58] GenomeInfoDb_1.40.1 IRanges_2.38.1 S4Vectors_0.42.1
[61] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 matrixStats_1.4.1
[64] BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] R.methodsS3_1.8.2 dichromat_2.0-0.1 tiff_0.1-12
[4] urlchecker_1.0.1 goftest_1.2-3 Biostrings_2.72.1
[7] HDF5Array_1.32.1 vctrs_0.6.5 digest_0.6.37
[10] png_0.1-8 proxy_0.4-27 pcaPP_2.0-5
[13] ggrepel_0.9.6 deldir_2.0-4 renv_1.0.11
[16] magick_2.8.5 hdrcde_3.4 MASS_7.3-61
[19] httpuv_1.6.15 scico_1.5.0 withr_3.0.2
[22] ellipsis_0.3.2 memoise_2.0.1 s2_1.1.7
[25] ggbeeswarm_0.7.2 refund_0.1-37 profvis_0.4.0
[28] systemfonts_1.1.0 ragg_1.3.3 lwgeom_0.2-14
[31] R.oo_1.27.0 KEGGREST_1.44.1 promises_1.3.2
[34] httr_1.4.7 rhdf5filters_1.16.0 ps_1.8.1
[37] rhdf5_2.48.0 rstudioapi_0.17.1 UCSC.utils_1.0.0
[40] units_0.8-5 miniUI_0.1.1.1 generics_0.1.3
[43] base64enc_0.1-3 processx_3.8.4 stars_0.6-7
[46] curl_6.0.1 zlibbioc_1.50.0 ScaledMatrix_1.12.0
[49] leafem_0.2.3 polyclip_1.10-7 GenomeInfoDbData_1.2.12
[52] SparseArray_1.4.8 fftwtools_0.9-11 xtable_1.8-4
[55] desc_1.4.3 pracma_2.4.4 S4Arrays_1.4.1
[58] tmaptools_3.1-1 irlba_2.3.5.1 colorspace_2.1-1
[61] filelock_1.0.3 isoband_0.2.7 later_1.4.1
[64] pbs_1.1 lattice_0.22-6 mapproj_1.2.11
[67] XML_3.99-0.17 svgPanZoom_0.3.4 class_7.3-22
[70] pillar_1.10.0 leafsync_0.1.0 compiler_4.4.1
[73] beachmat_2.20.0 RSpectra_0.16-2 stringi_1.8.4
[76] tensor_1.5 minqa_1.2.8 devtools_2.4.5
[79] plyr_1.8.9 fda_6.2.0 crayon_1.5.3
[82] abind_1.4-8 pals_1.9 locfit_1.5-9.10
[85] bit_4.5.0.1 terra_1.8-5 codetools_0.2-20
[88] textshaping_0.4.1 BiocSingular_1.20.0 crosstalk_1.2.1
[91] leaflet_2.2.2 e1071_1.7-16 fds_1.8
[94] mime_0.12 splines_4.4.1 Rcpp_1.0.13-1
[97] sparseMatrixStats_1.16.0 magic_1.6-1 blob_1.2.4
[100] BiocVersion_3.19.1 lme4_1.1-35.5 fs_1.6.5
[103] nnls_1.6 DelayedMatrixStats_1.26.0 pkgbuild_1.4.5
[106] gamm4_0.2-6 RcppHungarian_0.3 tibble_3.2.1
[109] Matrix_1.7-1 callr_3.7.6 statmod_1.5.0
[112] svglite_2.1.3 pkgconfig_2.0.3 tools_4.4.1
[115] aricode_1.0.3 cachem_1.1.0 RSQLite_2.3.9
[118] DBI_1.2.3 fastmap_1.2.0 grid_4.4.1
[121] usethis_3.1.0 shinydashboard_0.7.2 farver_2.1.2
[124] mgcv_1.9-1 wk_0.9.4 yaml_2.3.10
[127] deSolve_1.40 cli_3.6.3 purrr_1.0.2
[130] dbscan_1.2-0 lifecycle_1.0.4 uwot_0.2.2
[133] rainbow_3.8 mvtnorm_1.3-2 bluster_1.14.0
[136] sessioninfo_1.2.2 DropletUtils_1.24.0 BiocParallel_1.38.0
[139] gtable_0.3.6 rjson_0.2.23 parallel_4.4.1
[142] limma_3.60.6 jsonlite_1.8.9 edgeR_4.2.2
[145] bitops_1.0-9 bit64_4.5.2 spatstat.utils_3.1-1
[148] BiocNeighbors_1.22.0 ggside_0.3.1 metapod_1.12.0
[151] dqrng_0.4.1 zeallot_0.1.0 R.utils_2.12.3
[154] shiny_1.10.0 htmltools_0.5.8.1 rappdirs_0.3.3
[157] glue_1.8.0 XVector_0.44.0 RCurl_1.98-1.16
[160] RLRsim_3.1-8 mclust_6.1.1 classInt_0.4-10
[163] ks_1.14.3 jpeg_0.1-10 gridExtra_2.3
[166] sccore_1.0.5 boot_1.3-31 igraph_2.1.2
[169] R6_2.5.1 labeling_0.4.3 cluster_2.1.8
[172] pkgload_1.4.0 Rhdf5lib_1.26.0 memuse_4.2-3
[175] nloptr_2.1.1 DelayedArray_0.30.1 tidyselect_1.2.1
[178] vipor_0.4.7 maps_3.4.2.1 raster_3.6-30
[181] leidenAlg_1.1.4 AnnotationDbi_1.66.0 sfheaders_0.4.4
[184] rsvd_1.0.5 munsell_0.5.1 KernSmooth_2.23-24
[187] grpreg_3.5.0 htmlwidgets_1.6.4 spatstat.sparse_3.1-0
[190] remotes_2.5.0 ggnewscale_0.5.0 beeswarm_0.4.0