Pawsey pipeline

rebuttal_CellPress/PAWSEY_run_sccomp_script.R

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+
+library(targets)
+setwd('/home/zhanchen/From_scratch/HPC_sccomp/sccomp_on_cellNexus_1_0_10_2')
+
+tar_make(
+  # callr_function = NULL,
+  script = "/scratch/pawsey1192/zhanchen/HPC_sccomp/sccomp_on_cellNexus_1_0_10_2/_targets.R", 
+  store = "/scratch/pawsey1192/zhanchen/HPC_sccomp/sccomp_on_cellNexus_1_0_10_2/_targets", 
+  reporter = "verbose" #, callr_function = NULL
+) 
+
+
+
+
+
+
+
+system("rclone copy /scratch/pawsey1192/zhanchen/HPC_sccomp/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins___L3___disease_TRUE___immune_only_TRUE.rds UofA_Box:/Mangiola_ImmuneAtlas/taskforce_shared_folder/sccomp_on_cellNexus_1_0_10_2/")
+
+
+
+tar_meta(store = "/scratch/pawsey1192/zhanchen/HPC_sccomp/sccomp_on_cellNexus_1_0_10_2/_targets") |> 
+  arrange(desc(time)) |>
+  filter(!error |> is.na()) |> 
+  dplyr::select(name, error)
+
+
+
+
+library(tidyverse)
+library(sccomp)
+library(magrittr)
+library(glue)
+library(forcats)
+library(stringr)
+
+library(arrow)
+library(dplyr)
+library(duckdb)
+
+library(targets)
+
+x = tar_read(input_relative, store = "/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/_targets")
+
+
+tar_workspace(estimates_ae6e35523d730ab3, 
+              script = "/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/_targets.R", 
+              store = "/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/_targets"
+              )
+
+tar_meta(starts_with("estimates_"), store = "/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/_targets")
+
+# Age proportion prediciton
+estimates_age_bins |> 
+  sccomp_predict(
+    formula_composition = ~ 1 + age_bin*sex + (1 + age_bin*sex | tissue_groups), 
+    number_of_draws = 100,
+    summary_instead_of_draws = TRUE
+  ) |> 
+  mutate(age_bin = factor(
+    age_bin, 
+    c("Infancy", "Childhood", "Adolescence", "Young Adulthood", "Middle Age", "Senior"),
+    ordered = TRUE
+  )) |> 
+  mutate(age_bin_numeric = age_bin |> as.integer())  |> 
+  saveRDS("/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/prediction_age_bins.rds")
+
+system("~/bin/rclone copy /vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/prediction_age_bins.rds UofA_Box:/Mangiola_ImmuneAtlas/taskforce_shared_folder/")
+
+tar_read(formula_df, store = "/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/_targets")
+
+
+# For Hong
+estimate_age_bins = readRDS("/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins___L3.rds")
+estimate_age_bins = estimate_age_bins |> dplyr::select(-count_data)
+attr(estimate_age_bins, "fit") = NULL
+estimate_age_bins |> saveRDS("/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins_effect_tibble_only.rds")
+system("~/bin/rclone copy /vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins_effect_tibble_only.rds UofA_Box:/immune_map_disease/")
+
+# Save fit
+library(magrittr)
+estimate_age_bins = readRDS("/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins.rds")
+estimate_age_bins |> attr("fit") %$% save_object(file = "/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins_FIT_FOR_PORTABILITY.rds") 
+system("~/bin/rclone copy /vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins_FIT_FOR_PORTABILITY.rds UofA_Box:/Mangiola_ImmuneAtlas/taskforce_shared_folder/")
+estimate_age_bins |> attr("fit") = readRDS("/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins_FIT_FOR_PORTABILITY.rds")
+estimate_age_bins |> saveRDS("/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins.rds")
+system("~/bin/rclone copy /vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins.rds UofA_Box:/Mangiola_ImmuneAtlas/taskforce_shared_folder/")
+
+
+# estimate_age_bins |> saveRDS("/vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/estimates_age_bins.rds")
+system("~/bin/rclone copy /vast/projects/mangiola_immune_map/PostDoc/immuneHealthyBodyMap/sccomp_on_cellNexus_1_0_10_2/21_11_2024_sccomp_archive_before_factor_ordering/estimates_age_bins.rds UofA_Box:/Mangiola_ImmuneAtlas/taskforce_shared_folder/")
+
+# Benchmark
+tic()
+estimate_age_bins |> sccomp_test(contrasts = c(  "respiratory system" = "sexmale + `sexmale___respiratory system`",
+                                                 "blood" = "sexmale + `sexmale___blood`"))
+toc()
+
+
+estimate_age_bins |> 
+  sccomp_test()