Closed jovoni closed 8 months ago
I simulate a tissue with sampling but when I try to retrieve the sample forest via the get_samples_forest() function this error is raised
get_samples_forest()
Aiming cell id 132094 read Cell{id: 132093, parent_id: 46684, birth_time: 72.4925, species_id: 18} Error: Wrong cell file format.
Here is a reproducible example
library(rRACES) library(dplyr) library(ggplot2) library(patchwork) set.seed(777) # Prep simulation #### sim <- new(Simulation, seed = 777, save_snapshot = T) sim$update_tissue(1e3, 1e3) # Set the "border" growth model sim$duplicate_internal_cells <- FALSE # Set the death activation level to avoid drift sim$death_activation_level <- 50 # First and Second mutant #### sim$add_mutant(name = "Clone 1", # epigenetic_rates = c("+-" = 0.01, "-+" = 0.01), growth_rates = 1, death_rates = 0.01) sim$place_cell("Clone 1", 500, 500) # Let the simulation evolve until "A+" consists of 1000 cells sim$run_up_to_size("Clone 1", 1) # to observe muller from beginning sim$run_up_to_size("Clone 1", 1000) sim$add_mutant("Clone 2",growth_rates = 1.5, death_rates = 0.01) sim$mutate_progeny(sim$choose_cell_in("Clone 1"), "Clone 2") # Let the simulation evolve until "B+" consists of 3000 cells sim$run_up_to_size("Clone 2",3000) sim$update_rates("Clone 1",rates = c(growth = .001, death=0.01)) # Third mutant #### sim$add_mutant("Clone 3",growth_rates = 2, death_rates = 0.01) sim$mutate_progeny(sim$choose_cell_in("Clone 2"), "Clone 3") sim$update_rates("Clone 2",rates = c(growth = .001, death=0.01)) sim$run_up_to_size("Clone 3", 3000) sim$update_rates("Clone 1",rates = c(growth = 0, death=0.01)) sim$update_rates("Clone 2",rates = c(growth = 0, death=0.01)) sim$run_up_to_size("Clone 3", 5e4) #sim$run_up_to_size("C",1e5) plot_tissue(sim, num_of_bins = 300) # First sampling #### n_w <- n_h <- 50 ncells <- .99*n_w*n_h bbox <- sim$search_sample(c("Clone 3" = ncells), n_w, n_h) sim$sample_cells("A", bbox$lower_corner, bbox$upper_corner) sim$get_samples_forest() # sessionInfo() # R version 4.3.2 (2023-10-31) # Platform: aarch64-apple-darwin20 (64-bit) # Running under: macOS Sonoma 14.3.1 # # Matrix products: default # BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib # LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 # # locale: # [1] en_US.UTF-8 # # time zone: Europe/Rome # tzcode source: internal # # attached base packages: # [1] stats graphics grDevices utils datasets methods base # # other attached packages: # [1] patchwork_1.2.0 ggplot2_3.5.0 dplyr_1.1.4 rRACES_0.6.0 # # loaded via a namespace (and not attached): # [1] tidyselect_1.2.1 farver_2.1.1 fastmap_1.1.1 promises_1.2.1 digest_0.6.35 dotCall64_1.1-1 # [7] timechange_0.3.0 mime_0.12 lifecycle_1.0.4 ellipsis_0.3.2 processx_3.8.4 SeuratObject_5.0.1 # [13] magrittr_2.0.3 compiler_4.3.2 rlang_1.1.3 tools_4.3.2 utf8_1.2.4 knitr_1.45 # [19] labeling_0.4.3 htmlwidgets_1.6.4 curl_5.2.1 sp_2.1-3 pkgbuild_1.4.4 RColorBrewer_1.1-3 # [25] pkgload_1.3.4 miniUI_0.1.1.1 purrr_1.0.2 withr_3.0.0 desc_1.4.3 BiocGenerics_0.48.1 # [31] grid_4.3.2 stats4_4.3.2 fansi_1.0.6 urlchecker_1.0.1 RcppHNSW_0.6.0 profvis_0.3.8 # [37] xtable_1.8-4 colorspace_2.1-0 future_1.33.2 progressr_0.14.0 globals_0.16.3 scales_1.3.0 # [43] cli_3.6.2 crayon_1.5.2 remotes_2.5.0 ragg_1.3.0 generics_0.1.3 rstudioapi_0.16.0 # [49] future.apply_1.11.1 sessioninfo_1.2.2 ape_5.7-1 cachem_1.0.8 stringr_1.5.1 zlibbioc_1.48.2 # [55] parallel_4.3.2 XVector_0.42.0 vctrs_0.6.5 devtools_2.4.5 Matrix_1.6-5 callr_3.7.6 # [61] IRanges_2.36.0 S4Vectors_0.40.2 listenv_0.9.1 systemfonts_1.0.6 hexbin_1.28.3 glue_1.7.0 # [67] parallelly_1.37.1 spam_2.10-0 ps_1.7.6 codetools_0.2-19 stringi_1.8.3 RcppAnnoy_0.0.22 # [73] lubridate_1.9.3 gtable_0.3.4 later_1.3.2 munsell_0.5.1 tibble_3.2.1 pillar_1.9.0 # [79] htmltools_0.5.8 R6_2.5.1 textshaping_0.3.7 shiny_1.8.1 lattice_0.22-6 Biobase_2.62.0 # [85] memoise_2.0.1 httpuv_1.6.15 ggmuller_0.5.6 Rcpp_1.0.12 nlme_3.1-164 xfun_0.43 # [91] usethis_2.2.3 fs_1.6.3 pkgconfig_2.0.3 #
I simulate a tissue with sampling but when I try to retrieve the sample forest via the
get_samples_forest()function this error is raisedAiming cell id 132094 read Cell{id: 132093, parent_id: 46684, birth_time: 72.4925, species_id: 18} Error: Wrong cell file format.Here is a reproducible example