inst/app/init.R

In bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

options(cBioPortal.nav_ui =
          tagList(
            tabPanel("cBioPortal", uiOutput("cBioPortal"))
            #tabPanel("Dosimetry", uiOutput("dosimetry"))
            #tabPanel("Medical", uiOutput("medical"))

          )
)
options(Enrichment.nav_ui =
          tagList(
            tabPanel("Enrichment", uiOutput("Enrichment"))

          )
          )

# options(Tools.nav_ui =
#           tagList(
#             tabPanel("Tools", uiOutput("Tools"))
#
#           )
# )

## set default plots resolution
plot_width <- function(){
  if (is.null(input$plot_width)){
    r_data$plot_width <- 600
    }else{
      input$plot_width
    }
}

plot_height <- function(){
  if (is.null(input$plot_height)){
    r_data$plot_height <- 600
    }else{ input$plot_height
    }
}


## set default dataset
init_data <- function(env = r_data) {
  ## Based on discussion with Joe Cheng: Datasets can change over time
  ## so the data needs to be reactive value so the other reactive
  ## functions and outputs that depend on these datasets will know when
  ## they are changed

  ## Using an environment to assign data
  ## http://adv-r.had.co.nz/Environments.html#explicit-envs

  ## using a reactiveValues list to keep track of relevant app info
  ## that needs to be reactive
  r_data <- reactiveValues()
  r_info <- reactiveValues()

  df_names <- getOption("radiant.init.bioCancer", default = "epiGenomics")
  for (dn in df_names) {
    if (file.exists(dn)) {
      df <- load(dn) %>% get()
      dn <- basename(dn) %>%
      {gsub(paste0(".", tools::file_ext(.)), "", ., fixed = TRUE)}
    } else {
      df <- data(list = dn, package = "bioCancer", envir = environment()) %>% get()
      r_info[[paste0(dn, "_lcmd")]] <- glue::glue('{dn} <- data({dn}, package = "bioCancer", envir = environment()) %>% get()\nregister("{dn}")')
    }
    env[[dn]] <- df
    if (!bindingIsActive(as.symbol(dn), env = env)) {
      makeReactiveBinding(dn, env = env)
    }
    r_info[[paste0(dn, "_descr")]] <- attr(df, "description")
  }
  r_info[["datasetlist"]] <- basename(df_names)
  r_info[["url"]] <- NULL
  r_info
}