inst/app/old_v/v4.R

In sk-sahu/EcoGEx: Ecotype-specific Gene Expression

library(shiny)

ui <- fluidPage(
  
  titlePanel("Arabidopsis EcosGEx"),
  
  sidebarLayout(
    sidebarPanel(
      textInput("agi", "Entre your AGI ID:"),
      actionButton("find", "Find"),
      helpText("It will take some time. Be patient after you hit Find.")
    ),
    
    mainPanel(
      h3("Ecotype specific Gene Expression", align = "center"),
      dataTableOutput("mytable"),
      uiOutput("download")
    )
  )
  
)

###########################################################################
server <- function(input, output) {
  
  #Load packages
  library(data.table)
  library(maptools)
  library(maps)
  library(ggmap)
  library(ggplot2)
  
  observeEvent(input$find, {
    
    withProgress(message = 'Processing:', value = 0, {
      
      incProgress(1/2, detail = paste("Finding your gene"))
    
    #Read data.
    expr <- read.csv("expr.csv", sep = "\t", row.names = 1)
    cord <- read.csv("665_cord.csv")
    
    #Taking the AGI ID and process the table.
    agi_id <- toupper(input$agi)
    gene <- t(expr[agi_id,])
    gene_df <- as.data.frame(gene)
    gene_expr <- setDT(gene_df, keep.rownames = TRUE)[]
    colnames(gene_expr)[1] <- "gene_id"
    all <- merge(x=gene_expr, y=cord, by= "gene_id", all=TRUE)
    all_combined <- na.omit(all)
    colnames(all_combined)[1] <- "Ecotype_ID"
    
      incProgress(2/2, detail = paste("Printing table"))
    
    #Printing the table to screen
    output$mytable = renderDataTable({
      all_combined
    })
    
    
    #Downlord the file
    output$downloadData <- downloadHandler(
      filename = function() {
        paste(toupper(input$agi), ".csv", sep = "")
      },
      content = function(file) {
        write.csv(all_combined, file, row.names = FALSE)
      }
    )
    
    #Downlord button
    output$download <- renderUI({
      if(!is.null(input$agi)) {
        downloadButton("downloadData", "Download")
      }
    })
    
    })
  })  
}

shinyApp(ui = ui, server = server)