ui.R

library(shinythemes)

fluidPage(
  ####################### Browser icon
  headerPanel(
    tags$head(tags$link(rel = "icon", type = "image/png",
      href = "deploidTransLowSmall.ico")), windowTitle = "DEploid-ShinyApp"),

  ####################### Head image
  titlePanel(
    title = div(img(src = "deploidTrans.png", height = 93, width = 209,
      style = "margin:1px 1px"))),

  ####################### NAV BAR
  navbarPage(title = "", theme = shinytheme("cerulean"),

    ########## tabPanel 1. would be great to have a map here
    tabPanel("Sample infos",
      sidebarLayout(
        sidebarPanel(width = 3,
          shinyjs::useShinyjs(),
          radioButtons("inputSample", "What is this sample?",
                             c("Plasmodium Falciparum",
                               "Plasmodium Vivax")),
          hr(),
          uiOutput("inputOriginUI"),
          hr(),
          fileInput("inputVCFfile", "Choose VCF file",
                   accept = c("text", "ref", "txt")),
          actionButton("prepData", "Preparing data")
#          htmlOutput("panelSampleInfoExplainSample")
        ),
        mainPanel(width = 9,
          shinyjs::useShinyjs(),
          leafletOutput("panelSampleInfoMap", height = "530px")
        )
      )
     ),

    ############ tabPanel 2
    tabPanel("Sequence exploration",
      sidebarLayout(
        sidebarPanel(width = 3,
          sliderInput("panelDataTotalCoverageThreshold",
                      label = h4("Total coverage quantile threshold: "),
                      min = 0.9, max = 1, value = 0.995),
          sliderInput("panelDataTotalCoverageWindow",
                      label = h4("Window size for filtering: "),
                      min = 0, max = 50, value = 10),
          checkboxInput("advanceDEploidParameters",
                        label = h5("Advance parameters"), value = FALSE),
          conditionalPanel(
            condition = "input.advanceDEploidParameters == true",
            fluidRow(
              HTML("working progress ...")
            )
          ),
          actionButton("deconvData", "Deconvolution")
        ),
        mainPanel(width = 9,
          shinyjs::useShinyjs(),
          tabsetPanel(id = "data",
            tabPanel("Coverage distribution across the genome", value = "p1",
              fluidRow(column(12, dygraphOutput("panelDataTotalCoverage")))
            ),
            tabPanel("Allele read counts", value = "p3",
              fluidRow(column(2),
                column(8, plotlyOutput("panelDataAltVsRef"))
              )
#              htmlOutput("panelDataExplainTotalCoverage"),
            ),
            tabPanel("WSAF VS PLAF", value = "p4",
              fluidRow(column(2),
                column(6, plotlyOutput("panelDataWSAFVsPLAF")))
#              htmlOutput("panelDataExplainWSAFVsPLAF")
            ),
            tabPanel("WSAF Histogram", value = "p3",
              fluidRow(column(2),
                column(6, plotlyOutput("panelDataHistWSAF")))
#              htmlOutput("panelDataExplainHistWSAF"),
            )
          )
        )
      )
    ),

    ############ tabPanel 3
    tabPanel("Sequence deconvolution",
      sidebarLayout(
        sidebarPanel(width = 3,
          downloadButton("downloadHaplotypes", "Download haplotypes"),
          # HTML("<font color=\"blue\">TODO: interactive buttons.</font>"),
          uiOutput("inputCHROMUI"),
          # hr(),
          checkboxGroupInput("panelSequenceDeconWSAFVsPOSShades",
                             h5("Show Gene and Exon:"), c("Gene", "Exon")),
          hr(),
          checkboxInput("panelSequenceDeconWSAFVsPOSControlGene",
                        label = h5("Enable/Disable Gene Zoom"), value = FALSE),
          conditionalPanel(
            condition = "input.panelSequenceDeconWSAFVsPOSControlGene == true",
            fluidRow(
              column(5, radioButtons("panelSequenceDeconWSAFVsPOSGene",
                                     h5("Choose a Gene"),
                                     c("CRT", "DHFR", "DHPS", "Kelch", "MDR1",
                                       "Plasmepsin2&3"),
                                     selected = NULL)),
              column(7, uiOutput("inputGeneUI"))
          )
        )),
        mainPanel(width = 9,
          shinyjs::useShinyjs(),
          tabsetPanel(id = "deconvolution",
            tabPanel("Allele frequency across the genome", value = "p1",
              fluidRow(column(12, dygraphOutput("panelSequenceDeconWSAFVsPOS")))
            ),
            tabPanel("Expected vs observed allele frequency", value = "p1",
              fluidRow(column(3), column(5, align = "center",
                plotlyOutput("panelSequenceDeconObsVsExpWSAF")))),
            tabPanel("MCMC diagnostic",
              tabsetPanel(id = "mcmc",
                tabPanel("Proportions",
                         fluidRow(column(12, align = "center",
                                  plotlyOutput("panelMCMCProportions"))
                  )
                ),
                tabPanel("LLKs",
                         fluidRow(column(12, align = "center",
                                  plotlyOutput("panelMCMCLLK"))
                         )
                         )
              )
            )
          )
        )
      )
    ),

    ############ tabPanel 4
    navbarMenu("Documentation",
      tabPanel("Sample Infos", htmlOutput("infoPage")),
      tabPanel("Sequence Exploration", htmlOutput("dataPage")),
      tabPanel("Sequence Deconvolution", htmlOutput("dEploidPage")),
      tabPanel("Cite me", verbatimTextOutput("citeMe"))
    )

  )
)