mdsUI

server.R

@@ -1185,21 +1185,21 @@ shinyServer
     }
   })
   
-  output$acpUI <- renderUI({
+  output$mdsUI <- renderUI({
     validate(need(data16S(), ""))
     box(
       title = "Setting : " ,
       width = NULL,
       status = "primary",
       checkboxGroupInput(
-        "acpAxes",
+        "mdsAxes",
         label = "Axes : ",
         choices = seq(10),
         selected = c(1, 2),
         inline = TRUE
       ),
       selectInput(
-        "acpDist",
+        "mdsDist",
         label = "Distance : ",
         selected = "bray",
         choices = list(
@@ -1213,78 +1213,78 @@ shinyServer
         )
       ),
       selectInput(
-        "acpMethod",
+        "mdsMethod",
         label = "Method : ",
         selected = "MDS",
         choices = list("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")
       ),
-      textInput("acpTitle",
+      textInput("mdsTitle",
                 label = "Title : ",
                 value = "Samples ordination graphic"),
       selectInput(
-        "acpLabel",
+        "mdsLabel",
         label = "Label : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
-        "acpCol",
+        "mdsCol",
         label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
-        "acpShape",
+        "mdsShape",
         label = "Shape : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
-        "acpEllipse",
+        "mdsEllipse",
         label = "Ellipses : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
-        "acpRep",
+        "mdsRep",
         label = "Barycenters : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
-      collapsedBox(verbatimTextOutput("acpScript"), title = "RCode")
+      collapsedBox(verbatimTextOutput("mdsScript"), title = "RCode")
     )
   })
   
-  output$acpScript <- renderText({
+  output$mdsScript <- renderText({
     scriptArgs <- c(
       "physeq = data",
       glue(
-        "ordination = ordinate(data, method = \"{input$acpMethod}\", distance = \"{input$acpDist}\")"
+        "ordination = ordinate(data, method = \"{input$mdsMethod}\", distance = \"{input$mdsDist}\")"
       ),
-      glue("axes = c({glue_collapse(input$acpAxes, sep = ', ')})")
+      glue("axes = c({glue_collapse(input$mdsAxes, sep = ', ')})")
     )
-    if (!is.null(checkNull(input$acpCol))) {
-      scriptArgs <- c(scriptArgs, glue("color = \"{input$acpCol}\""))
+    if (!is.null(checkNull(input$mdsCol))) {
+      scriptArgs <- c(scriptArgs, glue("color = \"{input$mdsCol}\""))
     }
-    if (!is.null(checkNull(input$acpShape))) {
-      scriptArgs <- c(scriptArgs, glue("shape = \"{input$acpShape}\""))
+    if (!is.null(checkNull(input$mdsShape))) {
+      scriptArgs <- c(scriptArgs, glue("shape = \"{input$mdsShape}\""))
     }
-    if (!is.null(checkNull(input$acpRep))) {
-      scriptArgs <- c(scriptArgs, glue("replicate = \"{input$acpRep}\""))
+    if (!is.null(checkNull(input$mdsRep))) {
+      scriptArgs <- c(scriptArgs, glue("replicate = \"{input$mdsRep}\""))
     } else {
       scriptArgs <- c(scriptArgs, glue("replicate = NULL"))
     }
-    if (!is.null(checkNull(input$acpLabel))) {
-      scriptArgs <- c(scriptArgs, glue("label = \"{input$acpLabel}\""))
+    if (!is.null(checkNull(input$mdsLabel))) {
+      scriptArgs <- c(scriptArgs, glue("label = \"{input$mdsLabel}\""))
     }
-    if (!is.null(checkNull(input$acpTitle))) {
-      scriptArgs <- c(scriptArgs, glue("title = \"{input$acpTitle}\""))
+    if (!is.null(checkNull(input$mdsTitle))) {
+      scriptArgs <- c(scriptArgs, glue("title = \"{input$mdsTitle}\""))
     }
     script <- c(
       scriptHead,
       "# MultiDimensional scaling",
       glue("p <- plot_samples({glue_collapse(scriptArgs, sep=', ')})")
     )
-    if (!is.null(checkNull(input$acpEllipse))) {
+    if (!is.null(checkNull(input$mdsEllipse))) {
       script <- c(
         script,
         glue(
-          "p <- p + stat_ellipse(aes_string(group = \"{input$acpEllipse}\"))"
+          "p <- p + stat_ellipse(aes_string(group = \"{input$mdsEllipse}\"))"
         )
       )
     }
@@ -1293,31 +1293,31 @@ shinyServer
     return(glue_collapse(script, sep = "\n"))
   })
   
-  output$acp <- renderPlot({
+  output$mds <- renderPlot({
     validate(
       need(data16S(), "Requires an abundance dataset"),
-      need(length(input$acpAxes) == 2, "Requires two projections axes")
+      need(length(input$mdsAxes) == 2, "Requires two projections axes")
     )
     p <- plot_samples(
       data16S(),
       ordination = ordinate(
         data16S(),
-        method = input$acpMethod,
-        distance = input$acpDist
+        method = input$mdsMethod,
+        distance = input$mdsDist
       ),
-      axes = as.numeric(input$acpAxes),
-      title = checkNull(input$acpTitle),
-      color = checkNull(input$acpCol),
-      replicate = if (is.null(checkNull(input$acpRep))) {
+      axes = as.numeric(input$mdsAxes),
+      title = checkNull(input$mdsTitle),
+      color = checkNull(input$mdsCol),
+      replicate = if (is.null(checkNull(input$mdsRep))) {
         NULL
       } else {
-        checkNull(input$acpRep)
+        checkNull(input$mdsRep)
       },
-      shape = checkNull(input$acpShape),
-      label = checkNull(input$acpLabel)
+      shape = checkNull(input$mdsShape),
+      label = checkNull(input$mdsLabel)
     )
-    if (!is.null(checkNull(input$acpEllipse))) {
-      p <- p + stat_ellipse(aes_string(group = input$acpEllipse))
+    if (!is.null(checkNull(input$mdsEllipse))) {
+      p <- p + stat_ellipse(aes_string(group = input$mdsEllipse))
     }
     return(p + theme_bw())
   })

ui.R

@@ -155,8 +155,8 @@ shinyUI(dashboardPage(
       ),
       tabPanel(
         "MultiDimensional Scaling",
-        withLoader(plotOutput("acp", height = 700)),
-        uiOutput("acpUI")
+        withLoader(plotOutput("mds", height = 700)),
+        uiOutput("mdsUI")
       ),
       tabPanel(
         "Phylogenetic tree",