panel/richnessA

a0165c62 · Midoux Cedric · 9cbef098 · a0165c62 · a0165c62 · a0165c62
Commit a0165c62 authored 5 years ago by Midoux Cedric
Hide whitespace changes
Inline Side-by-side

Showing

with 154 additions and 154 deletions
+154 -154
--- a/panels/richnessA-server.R
+++ b/panels/richnessA-server.R
+output$richnessAUI <- renderUI({
+  validate(need(data16S(), ""))
+  box(
+    title = "Setting : " ,
+    width = NULL,
+    status = "primary",
+    checkboxGroupInput(
+      "richnessMeasures",
+      label = "Measures : ",
+      choices = c(
+        "Observed",
+        "Chao1",
+        "ACE",
+        "Shannon",
+        "Simpson",
+        "InvSimpson",
+        "Fisher"
+      ),
+      selected = c(
+        "Observed",
+        "Chao1",
+        "ACE",
+        "Shannon",
+        "Simpson",
+        "InvSimpson",
+        "Fisher"
+      ),
+      inline = TRUE
+    ),
+    radioButtons(
+      "richnessBoxplot",
+      label = "Representation : ",
+      choices = list(
+        "Dots only" = 1,
+        "Dots and boxplot" = 2,
+        "Boxplot only" = 3
+      ),
+      selected = 2,
+      inline = TRUE
+    ),
+    textInput("richnessTitle",
+              label = "Title : ",
+              value = "Alpha diversity graphics"),
+    selectInput(
+      "richnessX",
+      label = "X : ",
+      choices = c("..." = 0, sample_variables(data16S()))
+    ),
+    selectInput(
+      "richnessColor",
+      label = "Color : ",
+      choices = c("..." = 0, sample_variables(data16S()))
+    ),
+    selectInput(
+      "richnessShape",
+      label = "Shape : ",
+      choices = c("..." = 0, sample_variables(data16S()))
+    ),
+    collapsedBox(verbatimTextOutput("richnessAScript"), title = "RCode")
+  )
+})
+output$richnessAScript <- renderText({
+  if (!is.null(checkNull(input$richnessMeasures))) {
+    measures <-
+      glue("measures = c(\"{glue_collapse(input$richnessMeasures, sep='\", \"')}\")")
+  } else {
+    measures <- NULL
+  }
+  scriptArgs <- c("physeq = data", measures)
+  if (!is.null(checkNull(input$richnessX))) {
+    scriptArgs <- c(scriptArgs, glue("x = \"{input$richnessX}\""))
+  }
+  if (!is.null(checkNull(input$richnessColor))) {
+    scriptArgs <-
+      c(scriptArgs, glue("color = \"{input$richnessColor}\""))
+  }
+  if (!is.null(checkNull(input$richnessShape))) {
+    scriptArgs <-
+      c(scriptArgs, glue("shape = \"{input$richnessShape}\""))
+  }
+  if (!is.null(checkNull(input$richnessTitle))) {
+    scriptArgs <-
+      c(scriptArgs, glue("title = \"{input$richnessTitle}\""))
+  }
+  script <- c(
+    scriptHead,
+    "# Plot boxplot of alpha diversity",
+    glue(
+      "p <- plot_richness({glue_collapse(scriptArgs, sep=', ')})"
+    )
+  )
+  if (input$richnessBoxplot >= 2) {
+    script <- c(script,
+                "p <- p + geom_boxplot()")
+  }
+  if (input$richnessBoxplot <= 2) {
+    script <- c(script,
+                "p <- p + geom_point()")
+  }
+  script <- c(script, "", "plot(p)")
+  script <- c(script, "", "# Tables")
+  script <- c(
+    script,
+    glue(
+      "t <- estimate_richness({glue_collapse(c(\"data\", measures), sep=', ')})"
+    ),
+    "write.table(t, file = \"richness.tsv\", sep = \"\\t\", col.names = NA)"
+  )
+  return(glue_collapse(script, sep = "\n"))
+})
+output$richnessA <- renderPlot({
+  validate(need(data16S(),
+                "Requires an abundance dataset"))
+  p <- plot_richness(
+    physeq = data16S(),
+    x = ifelse(is.null(checkNull(
+      input$richnessX
+    )), "samples", input$richnessX),
+    color = checkNull(input$richnessColor),
+    shape = checkNull(input$richnessShape),
+    title = checkNull(input$richnessTitle),
+    measures = checkNull(input$richnessMeasures)
+  )
+  if (input$richnessBoxplot >= 2) {
+    p <- p + geom_boxplot()
+  }
+  if (input$richnessBoxplot <= 2) {
+    p <- p + geom_point()
+  }
+  return(p)
+})
+output$richnessATable <- renderUI({
+  validate(need(data16S(),
+                "Requires an abundance dataset"))
+  p(beautifulTable(data.frame(
+    SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2)
+  )))
+})
--- a/panels/richnessA-ui.R
+++ b/panels/richnessA-ui.R
+richnessA <- fluidPage(box(width = NULL, tabsetPanel(
+  tabPanel("Plots",
+           withLoader(plotOutput(
+             "richnessA", height = 700
+           )),
+           uiOutput("richnessAUI")),
+  tabPanel("Tables", withLoader(uiOutput("richnessATable")))
+)))
--- a/server.R
+++ b/server.R
@@ -12,6 +12,7 @@ shinyServer
  source("panels/histoFocus-server.R", local = TRUE)
  source("panels/heatmap-server.R", local = TRUE)
  source("panels/rarefactionCurve-server.R", local = TRUE)
+  source("panels/richnessA-server.R", local = TRUE)
  source("panels/tree-server.R", local = TRUE)
  checkNull <- function(x) {
@@ -317,150 +318,6 @@ shinyServer
    )
  })
-  output$richnessAUI <- renderUI({
-    validate(need(data16S(), ""))
-    box(
-      title = "Setting : " ,
-      width = NULL,
-      status = "primary",
-      checkboxGroupInput(
-        "richnessMeasures",
-        label = "Measures : ",
-        choices = c(
-          "Observed",
-          "Chao1",
-          "ACE",
-          "Shannon",
-          "Simpson",
-          "InvSimpson",
-          "Fisher"
-        ),
-        selected = c(
-          "Observed",
-          "Chao1",
-          "ACE",
-          "Shannon",
-          "Simpson",
-          "InvSimpson",
-          "Fisher"
-        ),
-        inline = TRUE
-      ),
-      radioButtons(
-        "richnessBoxplot",
-        label = "Representation : ",
-        choices = list(
-          "Dots only" = 1,
-          "Dots and boxplot" = 2,
-          "Boxplot only" = 3
-        ),
-        selected = 2,
-        inline = TRUE
-      ),
-      textInput("richnessTitle",
-                label = "Title : ",
-                value = "Alpha diversity graphics"),
-      selectInput(
-        "richnessX",
-        label = "X : ",
-        choices = c("..." = 0, sample_variables(data16S()))
-      ),
-      selectInput(
-        "richnessColor",
-        label = "Color : ",
-        choices = c("..." = 0, sample_variables(data16S()))
-      ),
-      selectInput(
-        "richnessShape",
-        label = "Shape : ",
-        choices = c("..." = 0, sample_variables(data16S()))
-      ),
-      collapsedBox(verbatimTextOutput("richnessAScript"), title = "RCode")
-    )
-  })
-  output$richnessAScript <- renderText({
-    if (!is.null(checkNull(input$richnessMeasures))) {
-      measures <-
-        glue("measures = c(\"{glue_collapse(input$richnessMeasures, sep='\", \"')}\")")
-    } else {
-      measures <- NULL
-    }
-    scriptArgs <- c("physeq = data", measures)
-    if (!is.null(checkNull(input$richnessX))) {
-      scriptArgs <- c(scriptArgs, glue("x = \"{input$richnessX}\""))
-    }
-    if (!is.null(checkNull(input$richnessColor))) {
-      scriptArgs <-
-        c(scriptArgs, glue("color = \"{input$richnessColor}\""))
-    }
-    if (!is.null(checkNull(input$richnessShape))) {
-      scriptArgs <-
-        c(scriptArgs, glue("shape = \"{input$richnessShape}\""))
-    }
-    if (!is.null(checkNull(input$richnessTitle))) {
-      scriptArgs <-
-        c(scriptArgs, glue("title = \"{input$richnessTitle}\""))
-    }
-    script <- c(
-      scriptHead,
-      "# Plot boxplot of alpha diversity",
-      glue(
-        "p <- plot_richness({glue_collapse(scriptArgs, sep=', ')})"
-      )
-    )
-    if (input$richnessBoxplot >= 2) {
-      script <- c(script,
-                  "p <- p + geom_boxplot()")
-    }
-    if (input$richnessBoxplot <= 2) {
-      script <- c(script,
-                  "p <- p + geom_point()")
-    }
-    script <- c(script, "", "plot(p)")
-    script <- c(script, "", "# Tables")
-    script <- c(
-      script,
-      glue(
-        "t <- estimate_richness({glue_collapse(c(\"data\", measures), sep=', ')})"
-      ),
-      "write.table(t, file = \"richness.tsv\", sep = \"\\t\", col.names = NA)"
-    )
-    return(glue_collapse(script, sep = "\n"))
-  })
-  output$richnessA <- renderPlot({
-    validate(need(data16S(),
-                  "Requires an abundance dataset"))
-    p <- plot_richness(
-      physeq = data16S(),
-      x = ifelse(is.null(checkNull(
-        input$richnessX
-      )), "samples", input$richnessX),
-      color = checkNull(input$richnessColor),
-      shape = checkNull(input$richnessShape),
-      title = checkNull(input$richnessTitle),
-      measures = checkNull(input$richnessMeasures)
-    )
-    if (input$richnessBoxplot >= 2) {
-      p <- p + geom_boxplot()
-    }
-    if (input$richnessBoxplot <= 2) {
-      p <- p + geom_point()
-    }
-    return(p)
-  })
-  output$richnessATable <- renderUI({
-    validate(need(data16S(),
-                  "Requires an abundance dataset"))
-    p(beautifulTable(data.frame(
-      SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2)
-    )))
-  })
  output$richnessBUI <- renderUI({
    validate(need(data16S(), ""))
    box(

--- a/ui.R
+++ b/ui.R
@@ -4,6 +4,7 @@ source("panels/histo-ui.R", local = TRUE)
 source("panels/histoFocus-ui.R", local = TRUE)
 source("panels/heatmap-ui.R", local = TRUE)
 source("panels/rarefactionCurve-ui.R", local = TRUE)
+source("panels/richnessA-ui.R", local = TRUE)
 source("panels/tree-ui.R", local = TRUE)
 shinyUI(dashboardPage(
@@ -114,16 +115,7 @@ shinyUI(dashboardPage(
      tabPanel("Rarefaction curves",
               rarefactionCurve),
      tabPanel(HTML("&alpha;-diversity"),
-               box(
+               richnessA),
-                 width = NULL, tabsetPanel(
-                   tabPanel("Plots",
-                            withLoader(plotOutput(
-                              "richnessA", height = 700
-                            )),
-                            uiOutput("richnessAUI")),
-                   tabPanel("Tables", withLoader(uiOutput("richnessATable")))
-                 )
-               )),
      tabPanel(
        HTML("&beta;-diversity"),
        selectInput(