inst/app/local_testing/new_app_test.R

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

library(shiny)
library(shinyFeedback)
library(markdown)

ui <- navbarPage("Arabidopsis EcoGEx", inverse = TRUE, collapsible = TRUE,

                 tabPanel("App", icon = icon("play-circle"),

                          sidebarLayout(
                            sidebarPanel(
                              useShinyFeedback(),
                              textInput("agi", "Entre your AGI:", value = "AT5G61590"),

                              helpText("AGI: Arabidopsis Gene Identifier."),
                              (textOutput("warning")),
                              tags$head(tags$style("#warning{color: red;}")),
                              actionButton("find", "Submit",
                                           icon = icon("angle-double-right")),
                              helpText("NOTE: It will take few seconds after Submiting.")
                            ),

                            mainPanel(h3("Ecotype specific Gene Expression",
                                         align = "center"),
                                      br(),

                                      tabsetPanel(type = "tabs",

                                                  # Interactive plot tab UI
                                                  tabPanel("Interactive Plot",
                                                           icon = icon("atlas"),
                                                           plotOutput("plot",
                                                                      click = "plot_click",
                                                                      height = 300,
                                                                      dblclick = "plot_dblclick",
                                                                      brush = brushOpts(
                                                                        id = "plot_brush",
                                                                        resetOnNew = TRUE
                                                                      )
                                                           ),
                                                           uiOutput("download_map"),
                                                           br(),
                                                           verbatimTextOutput("info"),
                                                           plotOutput("hist_plot")
                                                  ),

                                                  # Table Tab UI
                                                  tabPanel("Table", icon = icon("table"),
                                                           br(),
                                                           uiOutput("download_table"),
                                                           br(),
                                                           dataTableOutput("table")
                                                  ),

                                                  # Comparision Tab UI
                                                  tabPanel("Comparison",
                                                           icon = icon("bar-chart-o"),
                                                           uiOutput("dropdown_box1"),
                                                           uiOutput("dropdown_box2"),
                                                           uiOutput("dropdown_box3"),
                                                           plotOutput("bar_plot"),
                                                           verbatimTextOutput("value1"),
                                                           verbatimTextOutput("value2"),
                                                           verbatimTextOutput("value3")
                                                  )

                                      ) # tabstPanel ends here
                            ) # mainPanel ends here
                          ) # Sidebar pannedl ends here
                 ), # App tabPanel ends here

                 tabPanel("About",
                          icon = icon("info-circle") ,
                          includeMarkdown("about.md")
                 )

)

#######################   Server funtion starts from here ############################

# Loading packages
library(data.table)
library(maps)
library(ggplot2)
library(plyr)

server <- function(input, output) {

  observeEvent(input$agi, {
    feedbackWarning(
      "agi",
      condition = !grepl("[Aa][Tt][1-5][Gg]\\d\\d\\d\\d\\d",
                         input$agi),
      text = "Not an AGI"
    )

  })



  ranges <- reactiveValues(x = NULL, y = NULL)

  mp_table <- eventReactive(input$find, { # "Find" button event

    withProgress(message = 'Processing:', value = 0, {

      incProgress(1/2, detail = paste("Finding your gene")) ###################### Progress step 1

      # Read data (Time taking step)
      expr <- read.csv("data/GSE80744_gene_expression.csv", sep = "\t", row.names = 1)
      cord <- read.csv("data/665_geo_coordinates.csv")

      ##### Taking the AGI ID and process the final table (All Primary data) #####

      agi_id <- toupper(input$agi)
      gene <- t(expr[agi_id,]) # Making a list with Ecotype_id as row name and corospoding Expression value in one column for given agi_id as header.
      gene_df <- as.data.frame(gene)
      gene_expr <- setDT(gene_df, keep.rownames = TRUE)[] # data table made with Ecotype_id as col 1 and Expression value col 2
      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"
      colnames(all_combined)[2] <- "Gene_expression"

      all_combined

    }) # progress bar end

  })

  ############## Map Generation, printing and Download ####################

  # Generating Map
  mp <- reactive({
    all_combined <- mp_table()
    top20 <- head(arrange(all_combined, desc(all_combined$Gene_expression)) , n = 20)
    last20 <- tail(arrange(all_combined, desc(all_combined$Gene_expression)) , n = 20)

    mapWorld <- borders("legacy_world", colour="gray50", fill="gray50") # create a layer of borders
    mp <- ggplot() +   mapWorld #+ ggtitle(bquote("Exotype specific Gene expression of"== .(input$agi)))
    mp <- mp+ geom_point(aes(x=all_combined$longitude, y=all_combined$latitude) ,color="blue", size=3)+
      coord_cartesian(xlim = ranges$x, ylim = ranges$y, expand = FALSE)
    mp <- mp+ geom_point(aes(x=top20$longitude, y=top20$latitude) ,color="red", size=3)
    mp <- mp+ geom_point(aes(x=last20$longitude, y=last20$latitude) ,color="green", size=3)
    mp
  })

  # Printing Map to screen
  output$plot <- renderPlot({
    mp()
  })


  ################# Interactive Plot (Map) modifications #################

  # Plot Click
  output$info <- renderText({
    paste("\nLongitude=", input$plot_click$x,
          "\nLatitude=", input$plot_click$y
    )
  })

  # Zoom
  # When a double-click happens, check if there's a brush on the plot.
  # If so, zoom to the brush bounds; if not, reset the zoom.
  observeEvent(input$plot_dblclick, {
    brush <- input$plot_brush
    if (!is.null(brush)) {
      ranges$x <- c(brush$xmin, brush$xmax)
      ranges$y <- c(brush$ymin, brush$ymax)

    } else {
      ranges$x <- NULL
      ranges$y <- NULL
    }
  })

  ############ Printing the table to screen on table tab #########
  output$table = renderDataTable({
    mp_table()
  })

} # Server fucntion ends here

shinyApp(ui = ui, server = server)