Add the shiny app into the package

DESCRIPTION

@@ -8,6 +8,7 @@ Version: 1.0-1
 Author: Aurélie Siberchicot, Delphine Charif, Gabriel Terraz and Fabrice Vavre
 Maintainer: Aurélie Siberchicot <[email protected]>
 Imports: RColorBrewer
+Suggests: DT, shiny, shinyBS
 License: GPL (>=2.0)
 LazyData: yes
 Encoding: UTF-8

README.md

@@ -33,14 +33,22 @@ library(Mondrian)
 ```
 
 
+
 # The shiny app
 
 A web application (a `Shiny` application) is available to use the functionalities of the `Mondrian` package in an interactive way.
 In this application, two examples are shown. The user can also upload its own data and compute the `mondrian` function on it. 
 The display output can then be saved.
 
-The `MONDRIAN Shiny app` can be found at:
-http://lbbe-shiny.univ-lyon1.fr/MondrianShiny/
+`MondrianShiny` can be run on a R session, doing:
+```r
+shiny::runApp(system.file("MondrianShiny", package = "Mondrian"))
+```
+
+or online at:
+<a href="http://lbbe-shiny.univ-lyon1.fr/MondrianShiny/" target="_blank">http://lbbe-shiny.univ-lyon1.fr/MondrianShiny/</a>
+
+This shiny app is runing with the development version of `Mondrian`.
 
 
 

inst/MondrianShiny/global.R

@@ -0,0 +1,4 @@
+library(shinyBS)
+library(Mondrian)
+library(DT)
+library(tools)

inst/MondrianShiny/rinstall.txt

@@ -0,0 +1,4 @@
+install.packages("shinyBS",dependencies = TRUE, repos = "http://cran.univ-lyon1.fr")
+install.packages("DT",dependencies = TRUE, repos = "http://cran.univ-lyon1.fr")
+install.packages("RColorBrewer", dependencies = TRUE, repos = "http://cran.univ-lyon1.fr")
+install.packages("Mondrian", dependencies = TRUE, repos = "http://cran.univ-lyon1.fr")

inst/MondrianShiny/server.R

@@ -0,0 +1,201 @@
+shinyServer(function(input, output) {
+
+  ##########################################
+  ############### runex1 ###################
+  ##########################################
+  output$ex1plot <- renderPlot({
+    data(endosymbiont_1pop)
+    mondrian(endosymbiont_1pop, col = c("blue", "red", "yellow"))
+  })
+
+  output$ex1table <- renderPrint({
+    data(endosymbiont_1pop)
+    pdf("temp1.pdf")
+    res <- mondrian(endosymbiont_1pop, col = c("blue", "red", "yellow"))
+    dev.off()
+    if(file.exists("temp1.pdf"))
+      file.remove("temp1.pdf")
+    return(res)
+  })
+
+  output$ex1data <- renderDataTable({
+    data(endosymbiont_1pop)
+    DT::datatable(endosymbiont_1pop, options = list(pageLength = 10, searching = FALSE))
+  })
+
+
+
+  ##########################################
+  ############### runex2 ###################
+  ##########################################
+
+  output$ex2plot <- renderPlot({
+    data(endosymbiont_3pop)
+    mondrian(endosymbiont_3pop, pop = 1)
+  })
+
+  output$ex2table <- renderPrint({
+    data(endosymbiont_3pop)
+    pdf("temp2.pdf")
+    res <- mondrian(endosymbiont_3pop, pop = 1)
+    dev.off()
+    if(file.exists("temp2.pdf"))
+      file.remove("temp2.pdf")
+    return(res)
+  })
+
+  output$ex2data <- renderDataTable({
+    data(endosymbiont_3pop)
+    DT::datatable(endosymbiont_3pop, options = list(pageLength = 10, searching = FALSE))
+  })
+
+
+  ##########################################
+  ############## runmyplot #################
+  ##########################################
+  loaddata <- reactive({
+    input$doplot
+    isolate({
+
+      inFile <- input$file
+      if (! is.null(inFile)) {
+
+        ## data import
+        dd <- read.table(inFile$datapath, header = TRUE)
+        # TODO message d'erreur s'il n'y a pas les bonnes colonnes dans le fichier d'entrée
+        xx <- input$xlab
+        yy <- input$ylab
+        indiv <- input$indiv
+
+        if (input$pop == "multipop") {
+          mm <- ""
+          pp <- input$numpop
+
+          ## labels
+          ll <- NULL
+          ## colors
+          if (input$colors == "")
+            cc <- NULL
+          else
+            cc <- rep(strsplit(input$colors, " ")[[1]], length.out = NCOL(dd) - 1)
+
+
+        } else {
+          pp <- NULL
+          mm <- input$main  
+
+          ## labels
+          if (input$labels == "")
+            ll <- colnames(dd)
+          else
+            ll <- rep(strsplit(input$labels, " ")[[1]], length.out = NCOL(dd))
+
+          ## colors
+          if (input$colors == "")
+            cc <- NULL
+          else
+            cc <- rep(strsplit(input$colors, " ")[[1]], length.out = NCOL(dd))
+        }
+
+        return(list(dd = dd, ll = ll, cc = cc, pp = pp, xx = xx, yy = yy, mm = mm, indiv = indiv))
+      }
+    })
+  })
+
+
+  plotdata <- reactive({
+    res <- loaddata()
+    isolate({
+      if(is.null(res$pp) & ("pop" %in% names(res$dd))) {
+        return("Your dataset contains a 'pop' column indicating that your dataset comes from several sub-populations. You must indicate in which column the sub-population factor is in your dataset.")
+      } else if (!is.null(res$pp) & !("pop" %in% names(res$dd))) {
+        return("Your dataset don't contain a 'pop' column indicating that your dataset comes from a unique sub-population. You must indicate that your dataset come from 'only one population'.")
+      } else {
+        mm <- mondrian(res$dd, labels = res$ll, xlab = res$xx, ylab = res$yy, main = res$mm, col = res$cc, pop = res$pp, indiv = res$indiv)
+        return(mm)
+      }
+    })    
+  })
+
+
+  validateFile <- function(){
+    inFile <- input$file
+    extFile <- file_ext(inFile$name)
+    validate(
+      need(extFile == "txt" | extFile == "csv", "Only .txt or .csv files are allowed.")
+    )
+  }
+
+
+  output$mondrianplot <- renderPlot({
+    input$doplot
+    isolate({
+      inFile <- input$file
+      if (! is.null(inFile)) {
+        validateFile()
+        plotdata()
+      }
+    })
+  })
+
+
+  output$mondriantable <- renderPrint({
+    input$doplot
+    isolate({
+      inFile <- input$file
+      if (! is.null(inFile)) {
+        validateFile()
+        pdf("tempmondrian.pdf")
+        res <- plotdata()
+        dev.off()
+        if(file.exists("tempmondrian.pdf"))
+          file.remove("tempmondrian.pdf")
+        if (! is.null(res))
+          return(res)
+      }
+    })
+  })
+
+  output$mondriandata <- renderDataTable({
+    input$doplot
+    isolate({
+      inFile <- input$file
+      if (! is.null(inFile)) {
+        validateFile()
+        res <- as.data.frame(loaddata()$dd)
+        res <- res[complete.cases(res), ]
+        DT::datatable(res, options = list(pageLength = 10, searching = FALSE))
+      }
+    })
+  })
+
+
+
+
+
+
+
+  plotdata2 <- function() {
+    res <- loaddata()
+    mondrian(res$dd, labels = res$ll, xlab = res$xx, ylab = res$yy, main = res$mm, col = res$cc, pop = res$pp, indiv = res$indiv)
+  }
+
+  output$save <- downloadHandler(
+    filename = function() {
+      paste("mondrian_", Sys.Date(), ".png", sep = "")
+    },
+
+    content = function(file) {
+      png(file)
+      plotdata2()
+      dev.off()
+    },
+    contentType = 'image/png'
+  )
+
+  #   outputOptions(output, "save", suspendWhenHidden = FALSE)
+
+
+
+
+})