ui.R

# ui.R is running----
print("Run ui.R")

# init the app
source("./config.R")

fluidPage(
  theme = "style.css",
  title = "ShinyCNV", # webpage title
  h3("Shiny Copy Number Variation"), # top-left title
  p("Example Data: https://gitee.com/hiplot/ShinyCNV/blob/master/inputCNVs.txt"),
  conditionalPanel(
    "output.fileUploaded != true",
    selectInput("getHgVersion", "hg build:", c("hg18", "hg19", "hg38"), selected = "hg19", width = "100px")
  ),
  fluidRow(
    column(
      12,
      fileInput("cnvFile", "Choose CNV File"), # browse cnv file
      verbatimTextOutput("inputFileText")
    )
  ),
  p("Example SNP Data: https://gitee.com/hiplot/ShinyCNV/tree/master/SNPdata"),
  fluidRow(
    column(
      12,
      fileInput("SNPdata", "Choose SNPdata Files (Not require for demo)",
      multiple = TRUE), # browse cnv file
    )
  ),
  fluidRow(
    column(2, textInput("dataSuffix", "SNP Data Suffix:",
      placeholder = ".txt.gz", value = ".txt.gz", width = "200"
    )),
  ),
  hr(),
  conditionalPanel(
    "output.fileUploaded == true",
    sidebarLayout(
      # sidebarPanel----
      sidebarPanel(
        width = 4,
        DT::dataTableOutput("cnvTbl"),
        actionButton("getSNPdata", "Read in SNP data"),
        actionButton("prevCNV", "Prev CNV"),
        actionButton("nextCNV", "Next CNV"),
        verbatimTextOutput("SNPdataStatus", placeholder = TRUE),
        actionButton("addCNV", "Add CNV"),
        actionButton("setGermCNV", "Germ CNV"),
        actionButton("setCoveredCNV", "Covered CNV"),
        actionButton("setFalseCNV", "False CNV"),
        actionButton("setTrueCNV", "True CNV"),
        splitLayout(
          cellWidths = c(85, 80),
          actionButton("setChr", "Set Chr"),
          textInput("chr", "", placeholder = ""),
          actionButton("setCN", "Set CN"),
          textInput("copyNum", "", placeholder = ""),
          actionButton("setNormRate", "Set NR"),
          textInput("normRate", "", placeholder = "")
        ),
        # delete, set dup and clear SNP data----
        actionButton("delCNV", "Delete CNV"),
        # actionButton("setDupCNV", "Dup CNV"),
        actionButton("clearSNPdata", "Clear SNPdata")
      ),
      conditionalPanel(
        "output.SNPloaded == true",
        # mainPanel----
        mainPanel(
          width = 8,
          fluidRow(
            # BAF, LRR and gene list plot----
            column(12, plotOutput("caseBAF",
              height = bafLrrHeight, click = "caseBAF_click",
              brush = brushOpts("caseBAF_brush", delay = 500, delayType = "debounce", resetOnNew = T)
            )),
            column(12, plotOutput("ctrlBAF",
              height = bafLrrHeight, click = "ctrlBAF_click",
              brush = brushOpts("ctrlBAF_brush", delay = 500, delayType = "debounce", resetOnNew = T)
            )),
            column(12, plotOutput("caseLRR",
              height = bafLrrHeight, click = "caseLRR_click",
              brush = brushOpts("caseLRR_brush", delay = 500, delayType = "debounce", resetOnNew = T)
            )),
            column(12, plotOutput("ctrlLRR",
              height = bafLrrHeight, click = "ctrlLRR_click",
              brush = brushOpts("ctrlLRR_brush", delay = 500, delayType = "debounce", resetOnNew = T)
            )),
            column(12, plotOutput("genePlot", height = genePlotHeight, click = "genePlot_click")),

            # set position by selecting near point----
            column(2, selectInput("getChrPos", "Chr:", c("NA", "start", "end"))),
            column(2, textInput("position", "Pos:", placeholder = "", width = "200")),
            column(1, actionButton("setStart", "Set Start")),
            column(1, actionButton("setEnd", "Set End")),
            # select padding folds for CNV
            column(1, selectInput("getCnvPadX", "Padding X", c(0, 2, 4, 5, 8, 10, 20), selected = 4)),
            # max point number for showing BAF and LRR
            column(1, selectInput("maxSNPnum", "maxSNP", c(1000, 2000, 5000, 8000, 10000, 20000, 50000), selected = 10000)),
            # zoon out----
            column(1, actionButton("zoomOut2X", "Zoom out 2X")),
            column(1, actionButton("zoomOut5X", "Zoom out 5X")),
            column(1, actionButton("zoomOut10X", "Zoom out 10X"))
          ),
          column(2, tableOutput("geneTbl"))
        )
      )
    ),
    conditionalPanel(
      "output.SNPloaded == true",
      hr(),
      splitLayout(
        cellWidths = c(100, 200, 280, 120, 120, 120, 120, 100),
        actionButton("setChrGene", "Chr/Gene"),
        textInput("chrGeneName", "", placeholder = ""),
        verbatimTextOutput("spectPos", placeholder = TRUE),
        actionButton("zoomOut2XSpect", "Zoom out 2X"),
        actionButton("zoomOut5XSpect", "Zoom out 5X"),
        actionButton("zoomOut10XSpect", "Zoom out 10X"),
        actionButton("showCNV", "Show CNV"),
        actionButton("noCNV", "Hide CNV")
      ),
      plotOutput("spectrumPlot",
        brush = brushOpts("spect_brush", delay = 500, delayType = "debounce", resetOnNew = T)
      )
    )
  ),
  # allow read in cnv file again----
  tags$script('$( "#cnvFile" ).on( "click", function() { this.value = null; });')
)