R/CpG.GUI.R

In JoshuaTian/ChAMP: Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

if(getRversion() >= "3.1.0") utils::globalVariables(c("myLoad","probe. features.epic","probe.features"))

CpG.GUI <- function(CpG=rownames(myLoad$beta),
                    arraytype="450K")
{
  if(arraytype %in% c("EPIC", "EPICv2")) {
    data("probe.features.epicv2")
  } else if(arraytype == "EPICv1") {
    data("probe.features.epicv1")
  } else if(arraytype == "450K") { 
    data("probe.features")
  } else (
    stop("arraytype must be `EPICv2`, `EPICv1`, `450K`")
  )
  
  cgi.info <- table(probe.features[CpG,"cgi"])
  chromsome.info <- table(probe.features[CpG,"CHR"])
  feature.info <- table(probe.features[CpG,"feature"])
  type.info <- table(probe.features[CpG,"Type"])
  
  app <- shinyApp(
    ui = fluidPage(
      tags$head(tags$style("#cgi{height:40vh !important;}")),
      tags$head(tags$style("#chromsome{height:40vh !important;}")),
      tags$head(tags$style("#type{height:40vh !important;}")),
      tags$head(tags$style("#feature{height:40vh !important;}")),
      theme = shinytheme("readable"),
      titlePanel("CpG Overview"),
      tabsetPanel(
        tabPanel("CpG",
                 fluidRow(
                   #column(width = 3,
                   #       br(),
                   #       sidebarPanel(  width=12,
                   #                      numericInput('n', 'Number of obs', 100)
                   #                   )
                   #      ),
                   column(width = 12,
                          fluidRow(
                            column(width = 6,
                                   plotlyOutput("chromsome"),
                                   plotlyOutput("feature")
                            ),
                            column(width = 6,
                                   plotlyOutput("cgi"),
                                   plotlyOutput("type")
                            )
                          )
                   )#column 
                 )#fluidRow 
        )#tabPanel
      )#tabsetPanel
    ),#ui
    server = function(input, output){
      output$cgi <- renderPlotly({
        x <- list(
          title = ""
        )
        p <- plot_ly(x = names(cgi.info),
                     y = cgi.info,
                     name = "SF Zoo",
                     color = "orange",
                     type = "bar") %>%
          layout(xaxis = x)
      })
      output$chromsome <- renderPlotly({
        x <- list(
          title = ""
        )
        p <- plot_ly(x = paste("chr",names(chromsome.info),sep=""),
                     y = chromsome.info,
                     name = "SF Zoo",
                     type = "bar") %>%
          layout(xaxis = x)
      })
      output$feature <- renderPlotly({
        x <- list(
          title = ""
        )
        p <- plot_ly(x = names(feature.info),
                     y = feature.info,
                     name = "SF Zoo",
                     type = "bar") %>%
          layout(xaxis = x)
      })
      output$type <- renderPlotly({
        x <- list(
          title = ""
        )
        p <- plot_ly(x = names(type.info),
                     y = type.info,
                     name = "SF Zoo",
                     color = "orange",
                     type = "bar") %>%
          layout(xaxis = x)
      })
    }
  )
  runApp(app)
}