app.R

# xtlive.R
# ::rtemislive::
# 2024 EDG rtemis.org

# Shiny
# shiny::runApp("app.R")

# Setup
rtemisxt_version <- "0.0.3"
library(shiny)
library(bslib)
library(htmltools)
library(plotly)
library(rtemis)
library(rtemisbio)
source("globals.R")

# Source built-in datasets from data.R
source("data.R")

# Get names of all objects defined in data.R
builtin_names <- readLines("data.R") |>
  (\(z) grep("<-", x = z, value = TRUE))() |>
  (\(z) gsub(" <-.*", "", x = z))()

#' Create timeseries visualization shiny
#' Visualize timeseries data using `dplot3_xt()`
#'
#' Set verbosity to 1 to monitor app progress
#'
#' @param default_theme Character: "dark" or "light" theme
#' @param verbosity Integer: 0 = silent, 1 = verbose
#'
#' @author EDG
#' @export
#' @return A shiny app

xtlive <- function(
    default_theme = "dark",
    xt_plotly_height = "900px",
    verbosity = 0) {

  # Logo
  logo <- base64enc::dataURI(
    file = "./www/rtemisxt_gray.png", mime = "image/png"
  )

  # Version
  platform <- sessionInfo()[["platform"]]
  xtl <- paste0(
    "rtemisXt v", rtemisxt_version,
    " | ", "rtemisbio v", utils::packageVersion("rtemisbio"),
    " | ", "rtemis v", utils::packageVersion("rtemis"), # doesn't work in shinylive
    " | R v", version$major, ".", version$minor,
    " | running on ", platform
  )

  # Shinylive info
  shinylive_info <- if (substr(platform, 1, 4) == "wasm") {
    paste0(
      "<br><br>This application has been compiled to ",
      as.character(a("WebAssembly", href = "https://webassembly.org/", target = "_blank")),
      " using ",
      as.character(a("shinylive", href = "https://posit-dev.github.io/r-shinylive/", target = "_blank")),
      "<br>and is best viewed with the latest version of Chrome."
    )
  } else {
    NULL
  }

  # UI page_navbar ----
  ui <- function(request) {
    bslib::page_navbar(
      # Title ----
      title = list(
        logo = a(
          img(
            src = logo,
            width = "140px",
            height = "auto",
            alt = "rtemis"
          ),
          href = "https://rtemis.org/rtemisxt"
        )
      ),
      id = "rtemisxt",
      selected = "Welcome",
      footer = span(
        xtl,
        " © 2024 EDG",
        style = "display: block; text-align: center; margin-top: 1em; margin-bottom: 1em;"
      ),
      # Theme ----
      theme = bslib::bs_theme(
        `tooltip-opacity` = 1,
        `tooltip-border-radius` = "10px",
        `tooltip-padding-x` = "1rem",
        `tooltip-padding-y` = "1rem",
        `tooltip-font-size` = "1rem"
      ) |>
        bs_add_rules(sass::sass_file("www/rtemislive.scss")),
      # Window title ----
      window_title = "rtemis rtemisXt",
      # Language ----
      lang = "en",
      # Nav Panels ----
      ## [] Welcome ----
      bslib::nav_panel(
        title = "Welcome",
        icon = bsicons::bs_icon("stars"),
        bslib::card(
          h4("Welcome to rtemisXt.", style = "text-align: center;"),
          card_body(
            class = "d-inline text-center",
            HTML(paste0(
              "rtemisXt is a web interface for ",
              as.character(a("rtemis", href = "https://rtemis.org", target = "_blank")),
              ", <br>providing interactive visualization of timeseries data.",
              "<br><br>",
              rthelp_inline(
                "To get started, use the navigation tabs at the top.",
                title = "Welcome"
              ),
              shinylive_info
            )),
            br(), br(),
            bslib::card_image(
              file = "./www/rtemisxt_splash.png",
              alt = "rtemisXt",
              align = "center",
              border_radius = "all",
              fill = FALSE,
              width = "40%",
              class = "mx-auto"
            )
          )
        )
      ), # /nav_panel Welcome
      ## [] Timeseries Visualization ----
      bslib::nav_panel(
        title = "Timeseries",
        icon = bsicons::bs_icon("body-text"),
        card(
          full_screen = TRUE,
          class = "p-0",
          # allow items side by side ----
          card_header(
            class = "d-flex justify-content-end",
            # tooltip UI output ----
            uiOutput("ui_xt_tooltip"),
            # popover UI output ----
            uiOutput("ui_xt_popover")
          ),
          layout_sidebar(
            fillable = TRUE,
            # Data Load Sidebar ----
            sidebar = bslib::sidebar(
              uiOutput("ui_xt_load_switch"), # Switch between file upload and built-in data
              uiOutput("ui_xt_data_load"), # File upload or built-in data selection depending on switch
              uiOutput("ui_xt_data_info"), # Shows dataset info
              uiOutput("ui_xt_plot_button") # Click to plot
              # uiOutput("ui_xt_tooltip")
            ),
            # layout_sidebar(
            #   sidebar = bslib::sidebar(
            #     position = "right",
            #     # xt transformations
            #     "Timeseries Transformations"
            #   ),
            #   # Plot Output ----
            #   # for shinylive, do not use plotlyOutput directly in ui !!
            #   # fails when no plot is rendered, unlike shiny
            #   uiOutput("ui_dplot3_xt")
            # )
            uiOutput("ui_dplot3_xt")
          )
        )
      ), # /nav_panel Timeseries Visualization
      ## [] About ----
      bslib::nav_panel(
        title = "About",
        icon = bsicons::bs_icon("info-square"),
        bslib::card(
          card_image(
            file = "./www/rtemisbio.webp",
            href = "https://rtemis.org/rtemisbio",
            alt = "rtemisbio",
            align = "center",
            border_radius = "all",
            fill = FALSE,
            width = "54%",
            class = "mx-auto"
          ),
          div(
            class = "d-inline text-center",
            HTML(paste0(
              "Powered by ",
              as.character(a("rtemis", href = "https://rtemis.org", target = "_blank")),
              "."
            )),
            br(), br(),
            a(
              img(
                src = "rtemis_gray.png",
                alt = "rtemis",
                align = "center",
                width = "190px"
              ),
              href = "https://rtemis.org",
              target = "_blank"
            ),
            align = "center"
          )
        )
      ), # /nav_panel About
      bslib::nav_spacer(),
      bslib::nav_item(input_dark_mode(id = "dark_mode", mode = default_theme)),
      header = list(
        # busy indicators ----
        shinybusy::add_busy_spinner(
          spin = "orbit",
          color = "#00ffff",
          timeout = 200,
          position = "bottom-left",
          onstart = FALSE
        )
      )
    ) # /ui /bslib::page_navbar
  } # /ui function

  # Server ----
  server <- function(input, output, session) {
    # UI xt load switch ----
    output$ui_xt_load_switch <- shiny::renderUI({
      if (verbosity > 0) {
        message("Rendering ui_xt_load_switch")
      }
      # Radio buttons: built-in data vs upload file ----
      shiny::radioButtons(
        inputId = "xt_load_switch",
        label = "Data source",
        choices = list(
          `Built-in datasets` = "builtin",
          `File upload` = "upload"
        ),
        selected = "builtin"
      )
    })

    # UI xt Data ----
    output$ui_xt_data_load <- shiny::renderUI({
      req(input$xt_load_switch)
      if (input$xt_load_switch == "upload") {
        # Upload xt JSON file
        if (verbosity > 0) {
          message("Rendering ui_xt_data_load for file upload")
        }
        shiny::fileInput(
          inputId = "xt_file",
          label = "Upload xt file",
          buttonLabel = "Browse local files...",
        )
      } else {
        # Select built-in data stored in ./data/ directory
        if (verbosity > 0) {
          message("Rendering ui_xt_data_load for built-in data selection")
        }
        shiny::selectizeInput(
          inputId = "xt_builtin_data",
          label = "Select built-in xt dataset",
          choices = builtin_names,
          selected = builtin_names[1]
        )
      }
    }) # /ui_xt_data_load

    # UI for xt data info ----
    output$ui_xt_data_info <- shiny::renderUI({
      req(xt_obj())
      if (verbosity > 0) {
        message("Rendering ui_xt_data_info")
      }
      # inv comment
      bslib::card(
        bslib::card_title("xt Dataset Info", container = htmltools::h6),
        bslib::card_body(
          summarize_xt(xt_obj()),
          fillable = FALSE
        ) # /card_body
      ) # /card
    }) # /ui_xt_data_info

    # UI for plot action button ----
    output$ui_xt_plot_button <- shiny::renderUI({
      req(xt_obj())
      if (verbosity > 0) {
        message("Rendering ui_xt_plot_button")
      }
      bslib::input_task_button(
        "xt_plot_button",
        "Plot dataset",
        icon = bsicons::bs_icon("magic"),
        label_busy = "Drawing...",
        icon_busy = bsicons::bs_icon("clock-history"),
        type = "primary",
        auto_reset = TRUE
      )
    }) # /ui_xt_plot_button

    # Load Dataset ----
    xt_obj <- shiny::reactive({
      req(input$xt_load_switch)
      if (input$xt_load_switch == "upload") {
        # inv changed to "req(input$xt_file$datapath)": no help
        req(input$xt_file$datapath)
        if (verbosity > 0) {
          message("Loading xt data from file '", input$xt_file$datapath, "'")
        }
        # get file extension
        ext <- tools::file_ext(input$xt_file$datapath)
        dat <- if (ext == "json") {
          read.xtjson(input$xt_file$datapath)
        } else if (ext == "rds") {
          readRDS(input$xt_file$datapath)
        } else {
          stop("Unsupported file format")
        }
        if (verbosity > 0) {
          message("Loaded dataset of class '", class(dat)[1], "'")
        }
        return(dat)
      } else {
        # Load built-in data from data.R objects
        req(input$xt_builtin_data)
        if (verbosity > 0) {
          message("Loading built-in xt dataset '", input$xt_builtin_data, "'")
        }
        # Reading from data folder works fine in shiny app, not shinylive,
        # use objects from data.R instead
        # assign to dat object of name input$xt_builtin_data
        dat <- get(input$xt_builtin_data)
        if (verbosity > 0) {
          message("Loaded dataset of class '", class(dat)[1], "'")
        }
        return(dat)
      }
    }) # /xt_obj

    # dplot3 theme is "white" or "black" ----
    dplot3_theme <- shiny::reactive({
      req(input$dark_mode)
      if (input$dark_mode == "dark") {
        "black"
      } else {
        "white"
      }
    }) # /dplot3_theme

    # dplot3_theme() ----
    dplot3_theme <- shiny::reactive({
      req(input$dark_mode)
      if (input$dark_mode == "dark") {
        "darkgraygrid"
      } else {
        "whitegrid"
      }
    }) # /dplot3_theme

    # Render plotly ----
    output$dplot3_xt <- plotly::renderPlotly({
      req(xt_obj())
      if (verbosity > 0) {
        message("Rendering dplot3_xt of object with class '", class(xt_obj())[1], "'")
      }
      dplot3_xt(
        x = xt_obj(),
        yline.width = input$xt.linewidth,
        y2line.width = input$xt.linewidth,
        theme = dplot3_theme(),
        bg = input$plot.bg, # legend.bg defaults to transparent, this sets paper bg
        plot.bg = input$plot.bg,
        legend.x = 0,
        legend.xanchor = "left",
        show.rangeslider = input$show.rangeslider,
        margin = list(l = 75, r = 75, b = 75, t = 75),
      )
    }) |> # /dplot3_xt
      # bindEvent(input$xt_plot_button)
      bindEvent(input$xt_plot_button, input$xt_plot_update_button)

    # Create variable clicked that is TRUE after input$xt_plot_button is clicked
    clicked <- shiny::reactiveVal(FALSE)
    shiny::observeEvent(input$xt_plot_button, {
      clicked(TRUE)
    })

    # UI xt tooltip ----
    output$ui_xt_tooltip <- shiny::renderUI({
      if (clicked()) {
        bslib::tooltip(
          trigger = span(
            "Plot help", bsicons::bs_icon("info-circle", class = "text-info"),
            style = "text-align: right;",
            class = "rtanihi"
          ),
          div(
            rthelplist(
              c(
                "Hover over plot to see spike lines",
                # "Use top-right gear icon to access plot settings and click on 'Update rendering' to apply.",
                "Use top-right gear icon to access plot settings.",
                htmlEscape("To enter superscripts and subscripts in labs or units, use HTML tags, e.g. '<sup>2</sup>' and '<sub>i</sub>'.")
              )
            ),
            style = "text-align: left;"
          ), # /div rt-tooltip
          placement = "bottom"
        ) # /tooltip
      }
    }) # /ui_xt_tooltip

    # UI xt popover ----
    output$ui_xt_popover <- shiny::renderUI({
      if (clicked()) {
        popover(
          trigger = bsicons::bs_icon("gear", class = "ms-auto"),
          textInput(inputId = "xt.xlab", label = "X-axis label", value = ""),
          textInput(inputId = "xt.ylab", label = "Left Y-axis label", value = ""),
          textInput(inputId = "xt.y2lab", label = "Right Y-axis label", value = ""),
          textInput(inputId = "xt.xunits", label = "X-axis units", value = ""),
          textInput(inputId = "xt.yunits", label = "Left Y-axis units", value = ""),
          textInput(inputId = "xt.y2units", label = "Right Y-axis units", value = ""),
          textInput(inputId = "xt.firsttick", label = "First X-axis tick", value = "2"),
          textInput(inputId = "xt.ticksevery", label = "Show X-axis ticks every this many X values", value = "2"),
          sliderInput(inputId = "xt.linewidth", label = "Line width", min = 1, max = 10, value = 3),
          bslib::input_switch(
            id = "show.rangeslider",
            label = "Show rangeslider",
            value = TRUE
          ),
          shinyWidgets::colorPickr(
            "plot.bg",
            label = "Plot background",
            selected = ifelse(input$dark_mode == "dark", "#191919", "#FFFFFF")
          ),
          bslib::input_task_button(
            "xt_plot_update_button",
            "Update rendering",
            icon = bsicons::bs_icon("arrow-clockwise"),
            label_busy = "Drawing...",
            icon_busy = bsicons::bs_icon("clock-history"),
            type = "primary",
            auto_reset = TRUE
          ),
          title = "Plot settings",
          placement = "auto"
        ) # /popover
      }
    }) # /ui_xt_popover


    # UI dplot3_xt ----
    output$ui_dplot3_xt <- renderUI({
      if (clicked() == FALSE || is.null(xt_obj())) {
        rthelp(
          # "Select Data Source and Click 'Plot dataset' on the left.",
          "Select Data Source on the left.",
          title = "Timeseries Visualization "
        )
      } else {
        plotly::plotlyOutput(
          "dplot3_xt",
          width = "100%",
          height = xt_plotly_height
        )
      }
    }) # /ui_dplot3_xt
  } # /server

  # Shiny app ----
  shiny::shinyApp(ui = ui, server = server, enableBookmarking = "url")
} # xtlive

xtlive()