R/app_ui.R

In shinyTempSignal: Explore Temporal and Other Phylogenetic Signals

#' The application User-Interface
#'
#' @param request Internal parameter
#' @import shiny
#' @import shinydashboard

#' @importFrom shinyjs useShinyjs
#' @importFrom shinyWidgets colorPickr

app_ui <- function(request) {
  tagList(
    dashboardPage(
      skin = "yellow",
      dashboardHeader(title = "shinyTempSignal"),
      dashboardSidebar(
        radioButtons(
          inputId = "filetype",
          "choose your file type",
          choiceNames = list("Newick", "NEXUS", "BEAST", "Phylip"),
          choiceValues = list("Newick", "NEXUS", "Beast", "Phylip")
        ),
        fileInput("treefile", "choose a tree file"),
        textInput("regression", "Regular expression to extract sampling date from tip labels"),
        selectInput(
          "format",
          "Date format",
          c(
            "yy",
            "yyyy",
            "yyyy-MM-dd",
            "MM-dd-yyyy",
            "yyyy/MM/dd",
            "yyyy.MM.dd",
            "MM/dd/yyyy",
            "MM.dd.yyyy"
          )
        ),
        # tags$h4("This file is ",tags$strong("not necessary"),"."),
        fileInput(
          "outdata",
          "External data (optional)"
        ),
        actionButton("fileinput", "submit"),
        sidebarMenu(
          menuItem("Tree structure exploration", tabName = "tree"),
          menuItem("Sample Dates", tabName = "Dates"),
          menuItem("Temporal signal", tabName = "regression"),
          # menuItem("Subtree Temporal signal", tabName = "node"),
          # menuItem("Time_Series_Analysis", tabName = "time"),
          menuItem("Phylogenetic signal", tabName = "out")
          # menuItem("Subtree phylogenetic signal", tabName = "out_data_regression")
        )
      ),
      dashboardBody(
        tabItems(
          tabItem(
            tabName = "Dates",
            dataTableOutput("datetable"),
            downloadButton("download1", "download")
          ),
          # tabItem(
          #   tabName = "node",
          #   dataTableOutput("dataframe"),
          #   downloadButton("download2.table", "download")
          # ),
          # tabItem(
          #   tabName = "out_data_regression",
          #   dataTableOutput("out_dataframe"),
          #   downloadButton("download3.table", "download")
          # ),
          tabItem(
            tabName = "tree",
            box(
              plotOutput("plot1", click = "plotClick"),
              width = 8,
              height = 850
            ),
            box(
              width = 4,
              height = 850,
              sliderInput("height", "figure height:", 0, 5000, 835),
              fluidRow(
                column(width = 6, textInput("node", "subset_node")),
                column(width = 6, shinyWidgets::colorPickr("color3", label = "line color:", selected = "#020202"))
              ),
              fluidRow(
                column(width = 6, shinyWidgets::colorPickr("down_color", label = "down_color", selected = "#6a73cf")),
                column(width = 6, shinyWidgets::colorPickr("up_color", label = "up_color", selected = "#f26115"))
              ),
              sliderInput("size", "line size:", 0, 10, 1, step = 0.1),
              fluidRow(
                column(width = 4, checkboxInput("tip_point", "tip_point", FALSE)),
                column(width = 4, checkboxInput("tip", "tiplab", FALSE)),
                column(width = 4, checkboxInput("geom_nodelab", "node number", TRUE))
              ),
              sliderInput("tipsize", "tip_point_size:",
                0, 10, 3,
                step = 0.1
              ),
              fluidRow(
                column(width = 6, radioButtons(
                  inputId = "layout",
                  "tree layout",
                  choiceNames = list("rectangular", "roundrect", "slanted", "circular", "daylight", "ellipse", "fan"),
                  choiceValues = list("rectangular", "roundrect", "slanted", "circular", "daylight", "ellipse", "fan")
                )),
                column(width = 6, radioButtons(
                  inputId = "line_type", "tree line type",
                  choiceNames = list("solid", "twodash", "longdash", "dotted", "dashed", "dotdash", "blank"),
                  choiceValues = list("solid", "twodash", "longdash", "dotted", "dashed", "dotdash", "blank")
                ))
              ),
              radioButtons(
                inputId = "choose_analysis",
                "choose the point to display in the tree",
                choiceNames = list("only_tree", "Temporal_signal", "Phylogenetic_signal"),
                choiceValues = list("only_tree", "Temporal_signal", "Phylogenetic_signal")
              ),
              downloadButton("downloadplot1", "download(pdf)"),
              downloadButton("tree1", "download(newick)"),
            )
          ),
          tabItem(
            tabName = "regression",
            box(
              width = 8,
              plotOutput("plot2"),
              fluidRow(
                column(width = 3, downloadButton("downloadplot2", "download")),
                column(width = 3, actionButton("delete", "autodel")),
                column(width = 3, actionButton("reset", "Reset")),
                column(width = 3, textInput("temp_node", "node", value = ""))
              ),
              fluidRow(checkboxInput("plot_all", "plot whole tree regression", TRUE)),
              fluidRow(
                column(
                  6, numericInput("pvalue", "pvalue<:",
                    value = "0.05"
                  )
                ),
                column(
                  6, textInput("color2",
                    "line.color:",
                    value = "blue"
                  )
                )
              )
            ),
            box(
              width = 4,
              tableOutput("Summary"),
              downloadButton("download_dt2", "download")
            ),
            box(width = 8, plotOutput("multi_regression")),
            box(
              width = 4,
              textInput("multi_node", "input multi nodes(comma-separated)"),
              actionButton("update_button", "submit nodes")
            ),
            box(
              width = 12,
              dataTableOutput("dataframe"),
              downloadButton("download2.table", "download")
            ),
            dataTableOutput("outliers")
          ),
          tabItem(
            tabName = "out",
            box(
              width = 8,
              plotOutput("plot3"),
              downloadButton("downloadplot3", "download"),
              fluidRow(
                column(3, selectInput("x_var", "please choose your x var", choices = NULL), ),
                column(3, selectInput("y_var", "please choose your Y var", choices = NULL), ),
                column(3, actionButton("regression_btn", "update_regression_analysis")),
                column(3, checkboxInput("plot_all2", "plot whole tree regression", TRUE))
              ),
              fluidRow(
                column(width = 3, actionButton("delete2", "autodel")),
                column(width = 3, actionButton("reset2", "Reset")),
                column(width = 3, textInput("phylo_node", "node", value = ""))
              )
            ),
            box(
              width = 4,
              fluidRow(column(width = 12, tableOutput("Summary2")), downloadButton("download_dt_2", "download")),
              fluidRow(column(width = 12, verbatimTextOutput("correlation"))),
              radioButtons(
                inputId = "cortype",
                "choose your correltion type",
                choiceNames = list("PIC", "PGLS"),
                choiceValues = list("PIC", "PGLS")
              )
            ),
            box(width = 8, plotOutput("multi_regression2")),
            box(
              width = 4, textInput("multi_node2", " input multi nodes(comma-separated)"),
              actionButton("update_button2", "submit nodes")
            ),
            box(
              width = 12,
              dataTableOutput("out_dataframe"),
              downloadButton("download3.table", "download")
            ),
            box(dataTableOutput("outliers2"), width = 12),
            box(dataTableOutput("data_table"), width = 12)
          )
        )
      )
    )
  )
}


#' Add external Resources to the Application
#'
#' This function is internally used to add external
#' resources inside the Shiny application.
#'
#' @import shiny
#' @importFrom golem add_resource_path activate_js favicon bundle_resources
#' @noRd
golem_add_external_resources <- function() {
  add_resource_path(
    "www", app_sys("app/www")
  )

  tags$head(
    favicon(),
    bundle_resources(
      path = app_sys("app/www"),
      app_title = "sTSpkg"
    )
    # Add here other external resources
    # for example, you can add shinyalert::useShinyalert()
  )
}