inst/shiny/msn_explorer/ui.R

In grunwaldlab/poppr: Genetic Analysis of Populations with Mixed Reproduction

library(shiny)

shinyUI(fluidPage(

  # Application title
  title = "MSN poppr",
  titlePanel("Minimum spanning networks in poppr"),

  sidebarLayout(
    sidebarPanel(
      tags$h5("Status"),
      conditionalPanel(condition="!$('html').hasClass('shiny-busy')",
        tagAppendChild(tags$div(class="progress"),
        tagAppendChild(tags$div(class="progress-bar progress-bar-success", 
                       role="progressbar", `aria-valuenow`="100", 
                       `aria-valuemin`="0", `aria-valuemax`="100", 
                       style="width: 100%"), tags$strong("ready")))
      ),
      conditionalPanel(condition="$('html').hasClass('shiny-busy')",
        tagAppendChild(tags$div(class="progress"),
        tagAppendChild(tags$div(class="progress-bar progress-bar-striped active", 
                       role="progressbar", `aria-valuenow`="100", 
                       `aria-valuemin`="0", `aria-valuemax`="100", 
                       style="width: 100%"), tags$strong("loading")))
      ),
      tagAppendChildren(
        tags$div(style="display:inline-block"),
        list(
          actionButton("submit", "Go!", icon("check-circle")),
          actionButton("update-data", "reData", icon("refresh")),
          actionButton("update-graph", "reGraph", icon("refresh"))
        )
      ),
      # http://stackoverflow.com/a/21715813/2752888
      HTML("
      <h3>
        Data 
        <button type = 'button' class = 'btn btn-secondary btn-xs' data-toggle='collapse' data-target='#dparams' aria-expanded='true' aria-controls='dparams'> 
          show/hide
        </button>
      </h3>
      "),
      div(id = "dparams", class = "collapse in", 
        # h3("Data Parameters"),
        uiOutput("selectUI"),
        uiOutput("selectPops"),
        
        checkboxInput("genclone", "Convert to genclone?", TRUE),
        selectInput("distance", 
                    "Choose a distance calculation", 
                    choices = c("Dissimilarity",
                                "Bruvo",
                                "Nei",
                                "Rogers",
                                "Edwards",
                                "Provesti",
                                "Reynolds",
                                "Custom")
        ),
        conditionalPanel("input.distance == 'Custom'",
          uiOutput("customDist")
        ),
        conditionalPanel("input.distance == 'Bruvo'",
          selectInput("bruvo_model",
                      "Select a model for missing data",
                      choices = c("Genome Addition",
                                  "Genome Loss",
                                  "Infinite",
                                  "Average Addition/Loss"),
                      selected = "Average Addition/Loss"),
          textInput("replen", "SSR repeat lengths\n(comma separated or a valid R expression)", "1, 2, 3")
        ),
        conditionalPanel("input.distance != 'Bruvo'",
          uiOutput("distargsUI")
        ),
        checkboxInput("reticulate", "Include reticulations?", TRUE)
      ),
      HTML("
      <h3>
        Display
        <button type = 'button' class = 'btn btn-secondary btn-xs'  data-toggle='collapse' data-target='#gparams' aria-expanded='true' aria-controls='gparams'>
          show/hide
        </a>
      </h3>
      "),
      div(id = "gparams", class = "collapse in", 
        selectInput("layout", 
                    "Choose a layout", 
                    choices = c(
                      "layout_nicely",
                      "layout_randomly",
                      "layout_with_dh",
                      "layout_on_grid",
                      "layout_in_circle",
                      "layout_on_sphere",
                      "layout_as_tree",
                      "layout_as_star",
                      "layout_with_drl",
                      "layout_with_fr",
                      "layout_with_gem",
                      "layout_with_graphopt",
                      "layout_with_kk",
                      "layout_with_lgl",
                      "layout_with_mds",
                      "Custom")
        ),
        conditionalPanel("input.layout == 'Custom'",
          uiOutput("customLayout")
        ),
        checkboxInput("pop.leg", "Population legend", TRUE),
        checkboxInput("size.leg", "Node size legend", TRUE),
        checkboxInput("scale.leg", "Scale bar", TRUE), 
        sliderInput("greyslide",
                    "Grey scale",
                    min = 0,
                    max = 25,
                    value = 3,
                    step = 1
        ),
        sliderInput("nodescale",
                    "Node scale",
                    value = 10, 
                    min = 1,
                    max = 100,
                    step = 1),
        numericInput("seed", 
                     "Random Seed",
                     "69"
        ),
        radioButtons("ind_or_mlg", "Labels", 
                     choices = c("sample names", "MLGs"),
                     selected = "sample names", inline = TRUE
        ),
        textInput("inds", NULL, "ALL"),
        checkboxInput("mlgs", "Show MLG", FALSE),
        radioButtons("pal", "Indicate a color palette to be used",
                     choices=c("rainbow", 
                              "cm.colors", 
                              "topo.colors", 
                              "terrain.colors", 
                              "gray.colors",
                              "funky",
                              "spectral",
                              "seasun",
                              "azur",
                              "wasp",
                              "custom"), inline = TRUE
        ),
        conditionalPanel("input.pal == 'custom'",
          textInput("custom_pal", "Custom palette/function", "'purple'")
        ),
        numericInput("cutoff",
                     "Distance cutoff",
                     NULL,
                     step = 0.001
        ),
        checkboxInput("beforecut", "Keep graph position", TRUE)
      )
    ),


    mainPanel(
      tabsetPanel(
          tabPanel("Plot", plotOutput("plot", height = '600px')),
          tabPanel("Data", verbatimTextOutput("summary")),
          tabPanel("Command", verbatimTextOutput("cmd")),
          tabPanel("Save Plot",
             radioButtons("pdf_png", label = "Choose output filetype",
                          choices = c("pdf", "png"),
                          selected = "pdf",
                          inline = TRUE),
             conditionalPanel("input.pdf_png == 'pdf'",
               numericInput("pdf_plot_width", "Width (in)",
                           value = 7,
                           step = 0.1,
                           min = 1, 
                           max = 20),
               numericInput("pdf_plot_height", "Height (in)",
                           value = 7,
                           step = 0.1,
                           min = 1, 
                           max = 20),
               downloadButton("save_pdf", "Save PDF", class = "btn-info")
            ),
            conditionalPanel("input.pdf_png == 'png'",
              numericInput("png_plot_width", "Width (px)",
                          value = 400,
                          min = 1, 
                          max = 5000),
              numericInput("png_plot_height", "Height (px)",
                          value = 400,
                          min = 1, 
                          max = 5000),
              numericInput("png_res", "Resolution (dpi)",
                          value = 300,
                          min = 72,
                          max = 2000,
                          step = 1),
              downloadButton("save_png", "Save PNG", class = "btn-info")
            )
          ),
          tabPanel("Session Information",
                   verbatimTextOutput("infoRmation")
          )
    )
  )
)
))