title

server.R

@@ -27,7 +27,7 @@ shinyServer
       options = list(
         dom = "lBtip",
         pageLength = 10,
-        lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
+        lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')),
         buttons = list(
           'colvis',
           list(
@@ -172,6 +172,9 @@ shinyServer
         choices = rank_names(data16S()),
         inline = TRUE
       ),
+      textInput("barTitle",
+                label = "Title : ",
+                value = "OTU abundance barplot"),
       selectInput(
         "barGrid",
         label = "Subplot : ",
@@ -192,7 +195,8 @@ shinyServer
     p <- plot_bar(
       physeq = data16S(),
       fill = input$barFill,
-      x = ifelse(is.null(checkNull(input$barX)), "Sample", input$barX)
+      x = ifelse(is.null(checkNull(input$barX)), "Sample", input$barX),
+      title = checkNull(input$barTitle)
     )
     if (!is.null(checkNull(input$barGrid))) {
       p <-
@@ -349,6 +353,20 @@ shinyServer
         ),
         inline = TRUE
       ),
+      radioButtons(
+        "richnessBoxplot",
+        label = "Representation : ",
+        choices = list(
+          "Dots only" = 1,
+          "Dots and boxplot" = 2,
+          "Boxplot only" = 3
+        ),
+        selected = 2,
+        inline = TRUE
+      ),
+      textInput("richnessTitle",
+                label = "Title : ",
+                value = "Alpha diversity graphics"),
       selectInput(
         "richnessX",
         label = "X : ",
@@ -363,17 +381,6 @@ shinyServer
         "richnessShape",
         label = "Shape : ",
         choices = c("..." = 0, sample_variables(data16S()))
-      ),
-      radioButtons(
-        "richnessBoxplot",
-        label = "Representation : ",
-        choices = list(
-          "Dots only" = 1,
-          "Dots and boxplot" = 2,
-          "Boxplot only" = 3
-        ),
-        selected = 2,
-        inline = TRUE
       )
     )
   })
@@ -388,6 +395,7 @@ shinyServer
       )), "samples", input$richnessX),
       color = checkNull(input$richnessColor),
       shape = checkNull(input$richnessShape),
+      title = checkNull(input$richnessTitle),
       measures = checkNull(input$richnessMeasures)
     )
     if (input$richnessBoxplot >= 2) {
@@ -413,10 +421,13 @@ shinyServer
       width = NULL,
       status = "primary",
       selectInput(
-        "richnessOrder",
+        "richnessBOrder",
         label = "Sorting sample : ",
         choices = c("..." = 0, sample_variables(data16S()))
-      )
+      ),
+      textInput("richnessBTitle",
+                label = "Title : ",
+                value = "Beta diversity heatmap")
     )
   })
   
@@ -426,11 +437,11 @@ shinyServer
     beta <-
       melt(as(distance(data16S(), method = input$richnessBDist), "matrix"))
     colnames(beta) <- c("x", "y", "distance")
-    if (!is.null(checkNull(input$richnessOrder)))
+    if (!is.null(checkNull(input$richnessBOrder)))
     {
-      new_factor = as.factor(get_variable(data16S(), input$richnessOrder))
+      new_factor = as.factor(get_variable(data16S(), input$richnessBOrder))
       variable_sort <-
-        as.factor(get_variable(data16S(), input$richnessOrder)[order(new_factor)])
+        as.factor(get_variable(data16S(), input$richnessBOrder)[order(new_factor)])
       L = levels(reorder(sample_names(data16S()), as.numeric(new_factor)))
       beta$x <- factor(beta$x, levels = L)
       beta$y <- factor(beta$y, levels = L)
@@ -440,7 +451,7 @@ shinyServer
     }
     p <-
       ggplot(beta, aes(x = x, y = y, fill = distance)) + geom_tile()
-    p <- p + theme(
+    p <- p + ggtitle(input$richnessBTitle) + theme(
       axis.text.x = element_text(
         angle = 90,
         hjust = 1,
@@ -469,6 +480,9 @@ shinyServer
       checkboxInput("netwOrphan",
                     label = "Keep orphans",
                     value = TRUE),
+      textInput("netwTitle",
+                label = "Title : ",
+                value = "Beta diversity network"),
       selectInput(
         "netwCol",
         label = "Color : ",
@@ -507,7 +521,7 @@ shinyServer
       shape = checkNull(input$netwShape),
       label = checkNull(input$netwLabel),
       hjust = 2,
-      title = NULL
+      title = checkNull(input$netwTitle)
     )
     return(p)
   })
@@ -530,6 +544,7 @@ shinyServer
       step = 100,
       #step = input$rarefactionStep,
       color = checkNull(input$rarefactionColor),
+      label = checkNull(input$rarefactionLabel),
       se = FALSE
     )
     if (!is.null(checkNull(input$rarefactionGrid))) {
@@ -541,7 +556,7 @@ shinyServer
         p + geom_vline(xintercept = min(sample_sums(data16S())),
                        color = "gray60")
     }
-    return(p)
+    return(p + ggtitle(input$rarefactionTitle))
     
   })
   
@@ -559,11 +574,19 @@ shinyServer
       #   value = 100
       # ),
       checkboxInput("rarefactionMin", label = "Show min sample threshold", value = FALSE),
+      textInput("rarefactionTitle",
+                label = "Title : ",
+                value = "Rarefaction curves"),
       selectInput(
         "rarefactionColor",
         label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
+      selectInput(
+        "rarefactionLabel",
+        label = "Label : ",
+        choices = c("..." = 0, sample_variables(data16S()))
+      ),
       selectInput(
         "rarefactionGrid",
         label = "Subplot : ",
@@ -578,6 +601,9 @@ shinyServer
       title = "Setting : " ,
       width = NULL,
       status = "primary",
+      textInput("heatmapTitle",
+                label = "Title : ",
+                value = "Taxa heatmap by samples"),
       selectInput(
         "heatmapGrid",
         label = "Subplot : ",
@@ -637,6 +663,7 @@ shinyServer
       )[1:input$heatmapTopOtu]), data16S()),
       distance = input$heatmapDist,
       method = input$heatmapMethod,
+      title = checkNull(input$heatmapTitle),
       sample.order = checkNull(input$heatmapX),
       low = "yellow",
       high = "red",
@@ -672,6 +699,9 @@ shinyServer
       ),
       checkboxInput("treeRadial", label = "Radial tree", value = FALSE),
       checkboxInput("treeSample", label = "Show samples", value = TRUE),
+      textInput("treeTitle",
+                label = "Title : ",
+                value = "Phylogenetic tree"),
       selectInput(
         "treeCol",
         label = "Color : ",
@@ -704,7 +734,8 @@ shinyServer
       label.tips = checkNull(input$treeRank),
       sizebase = 5,
       ladderize = "left",
-      plot.margin = 0
+      plot.margin = 0,
+      title = checkNull(input$treeTitle)
     )
     if (checkNull(input$treeRadial)) {
       return(p + coord_polar(theta = "y"))
@@ -746,6 +777,9 @@ shinyServer
         selected = "MDS",
         choices = list("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")
       ),
+      textInput("acpTitle",
+                label = "Title : ",
+                value = "Samples ordination graphic"),
       selectInput(
         "acpLabel",
         label = "Label : ",
@@ -787,7 +821,7 @@ shinyServer
         distance = input$acpDist
       ),
       axes = as.numeric(input$acpAxes),
-      #c(1, 2),
+      title = checkNull(input$acpTitle),
       color = checkNull(input$acpCol),
       replicate = checkNull(input$acpRep),
       shape = checkNull(input$acpShape),