R/render_dashboard.R

In whtns/varbintools: Sequence Based Copy Number Detection Using Variable Bin Lengths

#' Render Varbin Dashboard
#'
#' @param rmarkdown
#' @param render
#'
#' @return
#' @export
#'
#' @examples
render_varbin_dashboard <- function(rmarkdown, render) {
  packages = c("flexdashboard", "here", "rmarkdown", "fs")
  # if a package is installed, it will be loaded
  # if any are not, the missing package(s) will be installed and loaded
  package.check <- lapply(packages, FUN = function(x) {

  tryCatch(expr = { library(x,character.only = TRUE)},
           error = function(e) {
           install.packages(x,dependencies=TRUE,type = "source",lib=.libPaths()[1],repos='http://cran.us.r-project.org')},
           finally = library(x,character.only = TRUE))

  })

  args <- commandArgs(trailingOnly = TRUE)

  Sys.setenv(RSTUDIO_PANDOC= "/usr/lib/rstudio-server/bin/pandoc")
  rmarkdown::render(paste(args[1], "/dashboard/cna_dashboard.Rmd", sep = ""),
                    output_format = "flexdashboard::flex_dashboard",
                    output_file = paste(dir_ls(here(),
                                               type = "directory",
                                               regexp = "final_result$",
                                               recursive = T),
                                        paste0("/",args[2], "_cna_dashboard.html"),
                                        sep = ""),
                    params = list(
                      directory = paste(args[1], "/bin", sep = "")
                    ))
}