reorganisation des onglets

server.R

@@ -130,7 +130,7 @@ shinyServer
     validate(
       need(
         data16S(),
-        "Firsly, you should select a demo dataset or upload an abundance BIOM file.\nFor example, with Galaxy, this one can be obtained at the end of FROGS workflows with 'FROGS BIOM to std BIOM' tools"
+        "Firstly, you should select a demo dataset or upload an abundance BIOM file.\nFor example, with Galaxy, a BIOM file can be obtained at the end of FROGS workflow with the 'FROGS BIOM to std BIOM' tool"
       )
     )
     data16S()
@@ -188,7 +188,7 @@ shinyServer
   
   output$histo <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p <- plot_bar(
       physeq = data16S(),
       fill = input$barFill,
@@ -251,7 +251,7 @@ shinyServer
   
   output$histoFocus <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p <- plot_composition(
       physeq = data16S(),
       taxaRank1 = input$focusRank,
@@ -311,7 +311,7 @@ shinyServer
   
   output$clust <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     plot_clust(
       physeq = data16S(),
       dist = input$clustDist,
@@ -380,7 +380,7 @@ shinyServer
   
   output$richnessA <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p <- plot_richness(
       physeq = data16S(),
       x = ifelse(is.null(checkNull(
@@ -401,7 +401,7 @@ shinyServer
   
   output$richnessATable <- renderUI({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p(beautifulTable(data.frame(
       SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2)
     )))
@@ -422,7 +422,7 @@ shinyServer
   
   output$richnessB <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     beta <-
       melt(as(distance(data16S(), method = input$richnessBDist), "matrix"))
     colnames(beta) <- c("x", "y", "distance")
@@ -493,7 +493,7 @@ shinyServer
   
   output$networkB <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     g <- make_network(
       data16S(),
       distance = input$richnessBDist,
@@ -514,7 +514,7 @@ shinyServer
   
   output$richnessBTable <- renderUI({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p(beautifulTable(data.frame(
       SAMPLE = sample_names(data16S()), round(as.matrix(
         distance(data16S(), method = input$richnessBDist)
@@ -524,7 +524,7 @@ shinyServer
   
   output$rarefactionCurve <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p <- ggrare(
       physeq = data16S(),
       step = 100,
@@ -630,7 +630,7 @@ shinyServer
   
   output$Heatmap <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p <- plot_heatmap(
       physeq = prune_taxa(names(sort(
         taxa_sums(data16S()), decreasing = TRUE
@@ -687,10 +687,10 @@ shinyServer
   
   output$tree <- renderPlot({
     validate(
-      need(data16S(), "Need an abundance dataset"),
+      need(data16S(), "Requires an abundance dataset"),
       need(
         phy_tree(data16S(), errorIfNULL = FALSE),
-        "Need an phylogenetic tree"
+        "Requires a phylogenetic tree"
       )
     )
     p <- plot_tree(
@@ -769,7 +769,7 @@ shinyServer
   
   output$acp <- renderPlot({
     validate(need(data16S(),
-                  "Need an abundance dataset"))
+                  "Requires an abundance dataset"))
     p <- plot_samples(
       data16S(),
       ordination = ordinate(

ui.R

@@ -79,7 +79,7 @@ shinyUI(dashboardPage(
         uiOutput("histUI")
       ),
       tabPanel(
-        "Focus barplot",
+        "Filtered barplot",
         plotOutput("histoFocus", height = 700),
         box(
           title = "Paramètres",
@@ -93,9 +93,14 @@ shinyUI(dashboardPage(
         )
       ),
       tabPanel(
-        "Clustering",
-        plotOutput("clust", height = 700),
-        uiOutput("clustUI")
+        "Heatmap",
+        plotOutput("Heatmap", height = 700),
+        uiOutput("HeatmapUI")
+      ),
+      tabPanel(
+        "Rarefaction curves",
+        plotOutput("rarefactionCurve", height = 700),
+        uiOutput("rarefactionCurveUI")
       ),
       tabPanel(HTML("α-diversity"),
                box(
@@ -138,9 +143,9 @@ shinyUI(dashboardPage(
         ))
       ),
       tabPanel(
-        "Rarefaction curves",
-        plotOutput("rarefactionCurve", height = 700),
-        uiOutput("rarefactionCurveUI")
+        "MultiDimensional Scaling",
+        plotOutput("acp", height = 700),
+        uiOutput("acpUI")
       ),
       tabPanel(
         "Phylogenetic tree",
@@ -148,17 +153,12 @@ shinyUI(dashboardPage(
         uiOutput("treeUI")
       ),
       tabPanel(
-        "Heatmap",
-        plotOutput("Heatmap", height = 700),
-        uiOutput("HeatmapUI")
-      ),
-      tabPanel(
-        "MultiDimensional Scaling",
-        plotOutput("acp", height = 700),
-        uiOutput("acpUI")
+        "Clustering",
+        plotOutput("clust", height = 700),
+        uiOutput("clustUI")
       ),
       tabPanel(
-        "News features ...",
+        "Help",
         div(
           "Questions, problems or comments regarding this application should be sent to ",
           a(href = "mailto:cedric.midoux@irstea.fr?subject=[Easy16S]", "cedric.midoux@irstea.fr")