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Adding Radar analysis and rix function
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| ### File generated by `rix::rix_init()` ### | ||
| # 1. Currently, system RStudio does not inherit environmental variables | ||
| # defined in `$HOME/.zshrc`, `$HOME/.bashrc` and alike. This is workaround to | ||
| # make the path of the nix store and hence basic nix commands available | ||
| # in an RStudio session | ||
| # 2. For nix-R session, remove `R_LIBS_USER`, system's R user library.`. | ||
| # This guarantees no user libraries from the system are loaded and only | ||
| # R packages in the Nix store are used. This makes Nix-R behave in pure manner | ||
| # at run-time. | ||
| { | ||
| is_rstudio <- Sys.getenv("RSTUDIO") == "1" | ||
| is_nix_r <- nzchar(Sys.getenv("NIX_STORE")) | ||
| if (isFALSE(is_nix_r) && isTRUE(is_rstudio)) { | ||
| cat("{rix} detected RStudio R session") | ||
| old_path <- Sys.getenv("PATH") | ||
| nix_path <- "/nix/var/nix/profiles/default/bin" | ||
| has_nix_path <- any(grepl(nix_path, old_path)) | ||
| if (isFALSE(has_nix_path)) { | ||
| Sys.setenv(PATH = paste(old_path, nix_path, sep = ":")) | ||
| } | ||
| rm(old_path, nix_path) | ||
| } | ||
| if (isTRUE(is_nix_r)) { | ||
| install.packages <- function(...) { | ||
| stop("You are currently in an R session running from Nix.\n", "Don't install packages using install.packages(),\nadd them to ", "the default.nix file instead.") | ||
| } | ||
| update.packages <- function(...) { | ||
| stop("You are currently in an R session running from Nix.\n", "Don't update packages using update.packages(),\n", "generate a new default.nix with a more recent version of R. ", "If you need bleeding edge packages, read the", "'Understanding the rPackages set release cycle and using ", "bleeding edge packages' vignette.") | ||
| } | ||
| remove.packages <- function(...) { | ||
| stop("You are currently in an R session running from Nix.\n", "Don't remove packages using `remove.packages()``,\ndelete them ", "from the default.nix file instead.") | ||
| } | ||
| current_paths <- .libPaths() | ||
| userlib_paths <- Sys.getenv("R_LIBS_USER") | ||
| user_dir <- grep(paste(userlib_paths, collapse = "|"), current_paths, fixed = TRUE) | ||
| new_paths <- current_paths[-user_dir] | ||
| .libPaths(new_paths) | ||
| rm(current_paths, userlib_paths, user_dir, new_paths) | ||
| } | ||
| rm(is_rstudio, is_nix_r) | ||
| } |
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| --- | ||
| title: "Analysis of all RADAR validation studies" | ||
| output: rmarkdown::html_vignette | ||
| vignette: > | ||
| %\VignetteIndexEntry{User guide} | ||
| %\VignetteEngine{knitr::rmarkdown} | ||
| %\VignetteEncoding{UTF-8} | ||
| --- | ||
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| ## Reproducible environment | ||
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| In case you want to make sure that you are creating the exact same output as presented in the publication, you need to create the reproducible environment using `rix` and `nix`. Using `rix`, you can run the following function to create your nix shell. | ||
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| ```{r eval = FALSE} | ||
| rix::rix( | ||
| r_ver = "latest", | ||
| r_pkgs = c("tidyverse", "tidyr", "purrr", "furrr", "gt","easystats","rlang", "DHARMa", "devtools", "patchwork", "rmarkdown"), | ||
| system_pkgs = NULL, | ||
| tex_pkgs = c("amsmath"), | ||
| git_pkgs = list(package_name = "xeredar", | ||
| repo_url = "https://github.com/basf/xeredar", | ||
| commit = "2b85763"), | ||
| ide = "rstudio", | ||
| project_path = "./vignettes", | ||
| overwrite = TRUE | ||
| ) | ||
| ``` | ||
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| Once the default.nix file was created in the path you specified in the command above (`project_path`) you need to type `nix-build` into the terminal. Once the shell was built you can open it via `nix-shell`. You can open Rstudio by first running this line in the terminal: `export QT_XCB_GL_INTEGRATION=none` and then running `rstudio`. Rstudio will open and you will have access to all files located at the path you specified in the `rix` function. You can run the script as usual. Through this approach, the code and results are reproducible. | ||
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| The following sections contain the code that needs to be executed to reproduce the analysis. | ||
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| ```{r} | ||
| # for(i in unique(RADAR_valid_data_table$Compound)){ | ||
| # for(j in unique(RADAR_valid_data_table$lab)){ | ||
| # dat <- RADAR_valid_data_table |> | ||
| # dplyr::filter(Compound == i & lab == j) | ||
| # if(!nrow(dat) == 0){ | ||
| # RADAR_valid_data[[paste0(i,j)]] <- dat | ||
| # } else{ | ||
| # next | ||
| # } | ||
| # } | ||
| # } | ||
| decreasing_alpha <- function(df, vector){ | ||
| for(i in vector){ | ||
| result <- xeredar::data_prep(df, row=FALSE, alpha = i, trim=FALSE, outlier = FALSE) | ||
| if(is.list(result)){ | ||
| break | ||
| } else{ | ||
| next | ||
| } | ||
| } | ||
| result[["alpha"]] <- i | ||
| return(result) | ||
| } | ||
| # RADAR_valid_data_table_spiked_unspiked <- purrr::map(RADAR_valid_data, spiked_unspiked) | ||
| changing_alpha <- sort(c(c(1,5) %o% 10^-(2:17), 0), decreasing = TRUE)[-1] | ||
| check <- function(list_dfs, id){ | ||
| result <- tryCatch({ | ||
| decreasing_alpha(list_dfs, changing_alpha) | ||
| }, error = function(e) { | ||
| list(error = paste("Error xeredar provides an error")) | ||
| }) | ||
| setNames(list(result), id) | ||
| } | ||
| anovas <- purrr::imap(xeredar::RADAR_valid_data_table_spiked_unspiked, ~ check(.x, .y)) |> purrr::flatten() | ||
| check_positive <- function(df){ | ||
| if(length(df) ==1){ | ||
| return(NA)} | ||
| if(df[["Monotonicity Test"]]$`Pr(>|t|)`[1] >= 0.01 & | ||
| df[["Monotonicity Test"]]$`Pr(>|t|)`[2] <= 0.01 ) { | ||
| return(df[["Dunnetts"]]) | ||
| } else if (length(unique(df$WilliamsIncrease$Y.Tilde)) - 1 > floor(nrow(df$WilliamsIncrease)/2) | | ||
| length(unique(df$WilliamsDecrease$Y.Tilde)) - 1 > floor(nrow(df$WilliamsDecrease)/2)) { | ||
| return(list(WilliamsIncrease = df[["WilliamsIncrease"]], WilliamsDecrease = df[["WilliamsDecrease"]])) | ||
| } else{ | ||
| return(df[["Dunnetts"]]) | ||
| } | ||
| } | ||
| resultList <- | ||
| anovas_unspiked <- anovas[stringr::str_detect(names(anovas), "Unspiked")] | ||
| anovas_spiked<- anovas[!stringr::str_detect(names(anovas), "Unspiked")] | ||
| results_Spiked <- purrr::map(anovas_spiked, check_positive) | ||
| results_Unspiked <- purrr::map(anovas_unspiked, check_positive) | ||
| Williams_Spiked <- !purrr::map_vec(results_Spiked, is.data.frame) | ||
| Williams_Unspiked <- !purrr::map_vec(results_Unspiked, is.data.frame) | ||
| significances <- function(df, Williams= FALSE){ | ||
| if(!is.list(df)){ | ||
| return(NA)} | ||
| if(Williams) { | ||
| if(TRUE %in% df[["WilliamsIncrease"]]$Sign){ | ||
| return("sign_Incr") | ||
| } | ||
| if(TRUE %in% df[["WilliamsDecrease"]]$Sign){ | ||
| return("sign_Decr") | ||
| } | ||
| else{ | ||
| return("Nonsignificant") | ||
| } | ||
| } | ||
| else{ | ||
| if(df[["adj p"]][length(df[["adj p"]])] < 0.05){ | ||
| if(df[["Estimate"]][length(df[["Estimate"]])] > 0){ | ||
| return("sign_Incr") | ||
| } else{ | ||
| return("sign_Decr") | ||
| } | ||
| } else{ | ||
| return("Nonsignificant") | ||
| } | ||
| } | ||
| } | ||
| significances_Spiked <- purrr::map2(results_Spiked, Williams_Spiked, significances) |> | ||
| dplyr::bind_rows(.id = "CompoundLab") |> | ||
| tidyr::pivot_longer( | ||
| cols = 1:44, | ||
| names_to = "CompoundLab", | ||
| values_to = "Spiked_sign" | ||
| ) |> | ||
| dplyr::mutate(CompoundLab = stringr::str_remove(CompoundLab,"_Spiked")) | ||
| significances_Unspiked <- purrr::map2(results_Unspiked, Williams_Unspiked, significances) |> | ||
| dplyr::bind_rows(.id = "CompoundLab") |> | ||
| tidyr::pivot_longer( | ||
| cols = 1:44, | ||
| names_to = "CompoundLab", | ||
| values_to = "Unspiked_sign" | ||
| ) |> | ||
| dplyr::mutate(CompoundLab = stringr::str_remove(CompoundLab,"_Unspiked")) | ||
| desired_order <- c( | ||
| "AmantadineWATCHFR", "AmantadineCEFAS", "AmantadineFIWI", "AmantadineFRAUNH", "AmantidineIDEA", | ||
| "LDopaWATCHFR", "ArabinoseWATCHFR", "CefuroximeWATCHFR", "CefuroximeCEFAS", "CefuroximeFIWI", | ||
| "CefuroximeFRAUNH", "CefuroximeIDEA", "CromolynWATCHFR", "CromolynCEFAS", "CromolynFIWI", | ||
| "CromolynIDEA", "AnastrazoleWATCHFR", "AnastrozoleCEFAS", "AnastrozoleFIWI", "AnastrozoleIDEA", | ||
| "ProchlorazWATCHFR", "DutasterideWATCHFR", "CyproteroneWATCHFR", "FenitrothionWATCHFR", | ||
| "FenitrothionCEFAS", "FenitrothionFIWI", "FenitrothionIDEA", "EstradiolWATCHFR", "mDHTWATCHFR", | ||
| "mDHTCEFAS", "mDHTFIWI", "mDHTFRAUNH", "mDHTIDEA", "TrenboloneWATCHFR", "LinuronWATCHFR", | ||
| "LinuronCEFAS", "LinuronFIWI", "LinuronFRAUNH", "LinuronIDEA", "VinclozolinWATCHFR", | ||
| "VinclozolinCEFAS", "VinclozolinFIWI", "VinclozolinFRAUNH", "VinclozolinIDEA" | ||
| ) | ||
| Result_Radar_valid <- dplyr::full_join(significances_Spiked, significances_Unspiked) |> | ||
| dplyr::mutate(`Known Mode of Action` = | ||
| dplyr::case_when( | ||
| stringr::str_detect(CompoundLab, "Amantadine|Amantidine|LDopa|Arabinose|Cefuroxime|Cromolyn")~ "no EAS MoA", | ||
| stringr::str_detect(CompoundLab, "Anastrozole|Anastrazole") ~ "steroidogenesis (anti-E): aromatase inhibitor (competitive)", | ||
| stringr::str_detect(CompoundLab, "Prochloraz") ~ "steroidogenesis (anti-E): aromatase inhibitor (transcriptional)", | ||
| stringr::str_detect(CompoundLab, "Dutasteride") ~ "steroidogenesis: 5alpha reductase inhibitor; AR antagonist (high conc.)", | ||
| stringr::str_detect(CompoundLab, "Cyproterone|Fenitrothion") ~ "anti-A: AR antagonist", | ||
| stringr::str_detect(CompoundLab, "Estradiol") ~ "E: ER agonist; steroidogenesis (anti-A): aromatase inducer", | ||
| stringr::str_detect(CompoundLab, "mDHT|Trenbolone") ~ "A: non-aromatizable AR agonist", | ||
| stringr::str_detect(CompoundLab, "Linuron") ~ "anti-A: AR antagonist; anti-E", | ||
| stringr::str_detect(CompoundLab, "Vinclozolin") ~ "anti-A: AR antagonist; E: weak ER agonist" | ||
| ), | ||
| CompoundLab = factor(CompoundLab, levels = desired_order)) |> | ||
| dplyr::arrange(CompoundLab) |> | ||
| dplyr::mutate(`Final Conclusion` = c('A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive','active', 'A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive','A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive', 'A(S)-inactive', 'S-active', 'S-active','S-active', 'inactive', 'inactive', 'A-active', 'A-active', 'A-active', 'A-active', 'A-active', 'A-ative','S-active', 'A-active', 'A-active', 'A-active', 'A-active', 'A-active', 'A-active', 'A-active', 'A-active''inactive', 'inactive', 'A-active', 'A-active', 'A-active', 'A-active', 'inactive', 'A-active')) |> | ||
| dplyr::relocate(c("CompoundLab", "Known Mode of Action", "Spiked_sign", "Unspiked_sign", "Final conclusion")) | ||
| gt::gt(Result_Radar_valid) | ||
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