R/schnapps-Main.R

In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

#' .schnappsEnv
#' Environment for package
.schnappsEnv <- new.env(parent = emptyenv())



#' shiny server relevant functions
#'
#' @details Shiny app for the analysis of single cell data
#'
#'
#' @param localContributionDir path to the directory(ies) that contain additional functionality
#' @param defaultValueSingleGene single gene name to used as a default value.
#' @param defaultValueMultiGenes comma separated list of gene names to be used as a default value.
#' @param defaultValueRegExGene regular Expression used for gene selection
#' @param DEBUG TRUE/FALSE whether to show debugging information on the console
#' @param DEBUGSAVE TRUE/FALSE where or not save internal data (very time consuming)
#' @param historyPath location (directory) where history directories and data will be stored.
#' @param defaultValues list of default values to use for inputs
#' @param workers number of CPUs to be used for normlization/clustering
#' @param launch.browser a function to call with the application's URL.
#'
#' @importFrom shinydashboard dashboardPage dashboardHeader dashboardSidebar sidebarMenu dashboardBody
#' tabItem menuSubItem menuItem
#' @importFrom shinyTree renderTree shinyTree
#' @importFrom DT DTOutput dataTableProxy
#' @importFrom dplyr '%>%'
#' @importFrom shiny shinyApp runApp
#'
#' @export schnapps
#'
#' @examples
#' # create example data
#' data("scEx", package = "SCHNAPPs")
#' save(file = "scEx.Rdata", list = "scEx")
#' # use "scEx.Rdata" with load data functionality within the shiny app
schnapps <- function(localContributionDir = "~/Rstudio/shHubgit/Dummy/",
                     defaultValueSingleGene = "CD3g",
                     defaultValueMultiGenes = "cd3g, cd4, cd8b, ms4a1, TCF4, LILRA2, LYZ, cd79a, bcl11b, IL32, hbb, nkg7,MNDA",
                     defaultValueRegExGene = "", # tip: '^CD7$|^KIT$; genes with min expression
                     DEBUG = FALSE,
                     DEBUGSAVE = FALSE,
                     historyPath = NULL,
                     defaultValues = list(),
                     port = NULL,
                     workers = 2,
                     launch.browser = getOption("shiny.launch.browser", interactive())
                     # ,
                     # historyFile = NULL

) {
 
   # on.exit({
  #   rm(list = c(".SCHNAPPs_locContributionDir",
  #        ".SCHNAPPs_defaultValueSingleGene",
  #        ".SCHNAPPs_defaultValueMultiGenes",
  #        ".SCHNAPPs_defaultValueRegExGene",
  #        ".SCHNAPPs_DEBUG",
  #        ".SCHNAPPs_DEBUGSAVE"),
  #      envir = .schnappsEnv)
  # })
  assign(".SCHNAPPs_locContributionDir", localContributionDir, envir = .schnappsEnv)
  assign(".SCHNAPPs_defaultValueSingleGene", defaultValueSingleGene, envir = .schnappsEnv)
  assign(".SCHNAPPs_defaultValueMultiGenes", defaultValueMultiGenes, envir = .schnappsEnv)
  assign(".SCHNAPPs_defaultValueRegExGene", defaultValueRegExGene, envir = .schnappsEnv)
  assign(".SCHNAPPs_DEBUG", DEBUG, envir = .schnappsEnv)
  assign(".SCHNAPPs_DEBUGSAVE", DEBUGSAVE, envir = .schnappsEnv)
  assign("DEBUG", DEBUG, envir = .schnappsEnv)
  assign("DEBUGSAVE", DEBUGSAVE, envir = .schnappsEnv)
  assign("historyPath", historyPath, envir = .schnappsEnv)
  assign("defaultValues", defaultValues, envir = .schnappsEnv)
  # assign("historyFile", historyFile, envir = .schnappsEnv)

  if (! "Wind" %in% installed.packages()){
    devtools::install_github("haowulab/Wind", build_opts = c("--no-resave-data"))
  }
  options(future.globals.maxSize= 2024^3)
  future::plan("multisession", workers = workers)
  packagePath <- find.package("SCHNAPPs", lib.loc = NULL, quiet = TRUE) %>% paste0("/app/")
  source(paste0(packagePath, "/serverFunctions.R"), local = TRUE)
  BiocParallel::register(safeBPParam(workers))
  
  # will be set during sourcing, but we need to define them, otherwise there will be a warning
  scShinyUI <- NULL
  scShinyServer <- NULL
  devscShinyApp <<- FALSE
  devscShinyApp <- FALSE
  source(paste0(packagePath, "/server.R"), local = TRUE)
  source(paste0(packagePath, "/ui.R"), local = TRUE)
  app <- shinyApp(ui = scShinyUI, server = scShinyServer, enableBookmarking = "server")
  runApp(app, port = port,launch.browser = launch.browser)
}

# library(SCHNAPPs)
#
# schnapps(localContributionDir = "~/Rstudio/__shHubgit/bjContributions",  defaultValueSingleGene = "cd52", defaultValueMultiGenes = "S100A4, CD52, S100A9, S100A8,")


#' Example data for schnapps app
#'
#' A dataset containing the prices and other attributes of almost 54,000
#' diamonds. The variables are as follows:
#'
#' * `scEx`: singlecellExperiment object
#'
#' @format A data frame with 53940 rows and 10 variables
#' @source <http://www.diamondse.info/>
"scExOrg"