Plot expression values according to design data.frame using DEGReport object

server.R

#https://gist.github.com/jcheng5/4050398
library(ggplot2)
options(shiny.maxRequestSize = -1)
shinyServer(function(input, output,session) {
  
  observe({
    if (is.null(input$files)) {
      # User has not uploaded a file yet
      return(NULL)
    }
    inFile <- input$files
    load(inFile$datapath)
    updateSelectInput(session, "srcgen", choices = colnames(deg[[2]]), selected="condition")
    updateSelectInput(session, "srccol", choices = colnames(deg[[2]]), selected="condition")
  })
  
  datasetInput <- reactive({
    if (input$do==0) {
      return(NULL)
    }else{
    data<-deg[[1]]
    des<-deg[[2]]
    exp<-(unlist(data[input$gene,]))
    gen<-des[,input$srcgen]
    col<-des[,input$srccol]

    exp<-list(data.frame(exp=exp,gen=gen,col=col))
    return(exp)
    }
    
  })
  
  output$distPlot <- renderPlot({
    if (input$do>0) {
      
    d<-datasetInput()[[1]]
    p <- ggplot(d, aes(factor(gen), exp)) +
      geom_boxplot(outlier.size = 0) + 
      geom_jitter(position=position_jitter(width=0.2),aes(factor(gen), exp,colour=col)) +
      stat_summary(fun.y=mean, geom="point",size=5)+
      scale_color_brewer(palette="Set1")+
      theme_bw(base_size = 16, base_family = "serif") +
      theme(axis.text.x=element_text(angle = 90, hjust = 1))+
      labs(list(title=input$gene,y="abundance",x=""))
    print(p)
    }
  })
})

ui.R

shinyUI(pageWithSidebar(
  headerPanel("Plot Expression using DEGReport package output"),
  sidebarPanel(
    fileInput("files", "File data", multiple=TRUE),
    selectInput("srcgen","Select genotype:", "Loading..."),
    selectInput("srccol","Select colours:", "Loading..."),
    textInput("gene", "Gene ID:", "ENSG00000000419"),
    actionButton("do","Update View")   
  ),
  mainPanel(
    plotOutput("distPlot")
  )
))