english

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(
@@ -45,9 +45,9 @@ shinyServer
     )
   }
   
-  source(
+  source({
     "https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/R/load-extra-functions.R"
-  )
+  })
   
   data16S <- reactive({
     if (input$demo != "input")
@@ -122,6 +122,7 @@ shinyServer
   output$rarefactionMin <- renderText({
     validate(need(input$fileBiom, ""), need(input$demo == "input", ""))
     paste("(min sample =", format(min(sample_sums(data16S(
+      
     ))), big.mark = " "), "reads)")
   })
   
@@ -129,7 +130,7 @@ shinyServer
     validate(
       need(
         data16S(),
-        "Merci de commencer par importer un fichier d'abondance au format BIOM. Celui-ci peut etre obtenu a l'issue du workflow FROGS avec l'operation 'FROGS BIOM to std BIOM'.\nVous pouvez egalement choisir un dataset de demo"
+        "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"
       )
     )
     data16S()
@@ -151,6 +152,7 @@ shinyServer
                    data.frame(OTU = taxa_names(data16S()), tax_table(data16S()))
                  )),
         tabPanel("sample_data",
+                 #as.data.frame(sapply(sample_data(data16S()), class)),
                  beautifulTable(
                    data.frame(SAMPLE = sample_names(data16S()), sample_data(data16S()))
                  ))
@@ -161,23 +163,24 @@ shinyServer
   output$histUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : ",
       width = NULL,
       status = "primary",
-      selectInput(
+      radioButtons(
         "barFill",
-        label = "Niveau taxo :",
-        choices = rank_names(data16S())
+        label = "Taxonomic rank : ",
+        choices = rank_names(data16S()),
+        inline = TRUE
       ),
       selectInput(
         "barGrid",
-        label = "Regroupement :",
+        label = "Subplot : ",
         choices = c("..." = 0, sample_variables(data16S()))
       )
       ,
       selectInput(
         "barX",
-        label = "X :",
+        label = "X : ",
         choices = c("..." = 0, sample_variables(data16S()))
       )
     )
@@ -185,7 +188,7 @@ shinyServer
   
   output$histo <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p <- plot_bar(
       physeq = data16S(),
       fill = input$barFill,
@@ -202,7 +205,7 @@ shinyServer
     validate(need(data16S(), ""))
     radioButtons(
       "focusRank",
-      label = "Niveau taxo :",
+      label = "Taxonomic rank : ",
       choices = rank_names(data16S())[-length(rank_names(data16S()))],
       inline = TRUE
     )
@@ -212,7 +215,7 @@ shinyServer
     validate(need(data16S(), ""))
     selectInput(
       "focusTaxa",
-      label = "Taxa :",
+      label = "Selected taxa : ",
       choices = unique(as.vector(tax_table(data16S(
         
       ))[, input$focusRank])),
@@ -224,11 +227,10 @@ shinyServer
     validate(need(data16S(), ""))
     sliderInput(
       "focusNbTaxa",
-      label = "Nombre de sous-taxons :",
+      label = "Number of sub-taxa : ",
       min = 0,
       #max = sum(tax_table(tax_glom(data16S(), rank_names(data16S())[1+as.integer(input$focusRank)]))[, as.integer(input$focusRank)]==input$focusTaxa)
-      max = 30
-      ,
+      max = 30,
       value = 10
     )
   })
@@ -236,20 +238,20 @@ shinyServer
   output$histFocusUIfocusGrid <- renderUI({
     validate(need(data16S(), ""))
     selectInput("focusGrid",
-                label = "Regroupement :",
+                label = "Subplot : ",
                 choices = c("..." = 0, sample_variables(data16S())))
   })
   
   output$histFocusUIfocusX <- renderUI({
     validate(need(data16S(), ""))
     selectInput("focusX",
-                label = "X :",
+                label = "X : ",
                 choices = c("..." = 0, sample_variables(data16S())))
   })
   
   output$histoFocus <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p <- plot_composition(
       physeq = data16S(),
       taxaRank1 = input$focusRank,
@@ -269,12 +271,12 @@ shinyServer
   output$clustUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       selectInput(
         "clustDist",
-        label = "Distance :",
+        label = "Distance : ",
         choices = list(
           "bray",
           "jaccard",
@@ -287,7 +289,7 @@ shinyServer
       ),
       selectInput(
         "clustMethod",
-        label = "Methode :",
+        label = "Method : ",
         choices = list(
           "ward.D2",
           "ward.D",
@@ -301,7 +303,7 @@ shinyServer
       ),
       selectInput(
         "clustCol",
-        label = "Couleur :",
+        label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       )
     )
@@ -309,7 +311,7 @@ shinyServer
   
   output$clust <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     plot_clust(
       physeq = data16S(),
       dist = input$clustDist,
@@ -321,12 +323,12 @@ shinyServer
   output$richnessAUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       checkboxGroupInput(
         "richnessMeasures",
-        label = "Mesures :",
+        label = "Measures : ",
         choices = c(
           "Observed",
           "Chao1",
@@ -349,26 +351,26 @@ shinyServer
       ),
       selectInput(
         "richnessX",
-        label = "X :",
+        label = "X : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "richnessColor",
-        label = "Couleur :",
+        label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "richnessShape",
-        label = "Forme :",
+        label = "Shape : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       radioButtons(
         "richnessBoxplot",
-        label = "Representation :",
+        label = "Representation : ",
         choices = list(
-          "Points seuls" = 1,
-          "Boxplot et points" = 2,
-          "Boxplot seul" = 3
+          "Dots only" = 1,
+          "Dots and boxplot" = 2,
+          "Boxplot only" = 3
         ),
         selected = 2,
         inline = TRUE
@@ -378,7 +380,7 @@ shinyServer
   
   output$richnessA <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p <- plot_richness(
       physeq = data16S(),
       x = ifelse(is.null(checkNull(
@@ -399,7 +401,7 @@ shinyServer
   
   output$richnessATable <- renderUI({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p(beautifulTable(data.frame(
       SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2)
     )))
@@ -407,12 +409,12 @@ shinyServer
   
   output$richnessBUI <- renderUI({
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       selectInput(
         "richnessOrder",
-        label = "Ordre de tri des echantillons :",
+        label = "Sorting sample : ",
         choices = c("..." = 0, sample_variables(data16S()))
       )
     )
@@ -420,7 +422,7 @@ shinyServer
   
   output$richnessB <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     beta <-
       melt(as(distance(data16S(), method = input$richnessBDist), "matrix"))
     colnames(beta) <- c("x", "y", "distance")
@@ -454,32 +456,32 @@ shinyServer
   output$networkBUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       sliderInput(
         "netwMax",
-        label = "Cutoff :",
+        label = "Threshold : ",
         min = 0,
         max = 1,
         value = 0.7
       ),
       checkboxInput("netwOrphan",
-                    label = "Garder les points orphelins",
+                    label = "Keep orphans",
                     value = TRUE),
       selectInput(
         "netwCol",
-        label = "Couleur :",
+        label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "netwShape",
-        label = "Forme :",
+        label = "Shape : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "netwLabel",
-        label = "Label :",
+        label = "Label : ",
         choices = c(
           "..." = 0,
           "Sample name" = "value",
@@ -491,7 +493,7 @@ shinyServer
   
   output$networkB <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     g <- make_network(
       data16S(),
       distance = input$richnessBDist,
@@ -512,7 +514,7 @@ shinyServer
   
   output$richnessBTable <- renderUI({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p(beautifulTable(data.frame(
       SAMPLE = sample_names(data16S()), round(as.matrix(
         distance(data16S(), method = input$richnessBDist)
@@ -522,7 +524,7 @@ shinyServer
   
   output$rarefactionCurve <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p <- ggrare(
       physeq = data16S(),
       step = 100,
@@ -546,25 +548,25 @@ shinyServer
   output$rarefactionCurveUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       # sliderInput(
       #   "rarefactionStep",
-      #   label = "Etapes de calcul :",
+      #   label = "Etapes de calcul : ",
       #   min = 1,
       #   max = 1000,
       #   value = 100
       # ),
-      checkboxInput("rarefactionMin", label = "Afficher le seuil de l'echantillon minimal", value = FALSE),
+      checkboxInput("rarefactionMin", label = "Show min sample threshold", value = FALSE),
       selectInput(
         "rarefactionColor",
-        label = "Couleur :",
+        label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "rarefactionGrid",
-        label = "Regroupement :",
+        label = "Subplot : ",
         choices = c("..." = 0, sample_variables(data16S()))
       )
     )
@@ -573,29 +575,29 @@ shinyServer
   output$HeatmapUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       selectInput(
         "heatmapGrid",
-        label = "Regroupement :",
+        label = "Subplot : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "heatmapX",
-        label = "X :",
+        label = "X : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       sliderInput(
         "heatmapTopOtu",
-        label = "Selection des n OTU les plus abondant :",
+        label = "Show the n most abundant OTU : ",
         min = 1,
         max = ntaxa(data16S()),
         value = 250
       ),
       selectInput(
         "heatmapDist",
-        label = "Distance :",
+        label = "Distance : ",
         selected = "bray",
         choices = list(
           "bray",
@@ -609,7 +611,7 @@ shinyServer
       ),
       selectInput(
         "heatmapMethod",
-        label = "Methode :",
+        label = "Method : ",
         selected = "NMDS",
         choices = list(
           "NMDS",
@@ -628,7 +630,7 @@ shinyServer
   
   output$Heatmap <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p <- plot_heatmap(
       physeq = prune_taxa(names(sort(
         taxa_sums(data16S()), decreasing = TRUE
@@ -650,12 +652,12 @@ shinyServer
   output$treeUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       radioButtons(
         "treeRank",
-        label = "Niveau taxonomique légendé :",
+        label = "Taxonomic rank captioned : ",
         choices = c(aucun = "",
                     rank_names(data16S()),
                     OTU = "taxa_names"),
@@ -663,21 +665,21 @@ shinyServer
       ),
       sliderInput(
         "treeTopOtu",
-        label = "Selection des n OTU les plus abondant :",
+        label = "Show the n most abundant OTU : ",
         min = 1,
         max = ntaxa(data16S()),
         value = 20
       ),
-      checkboxInput("treeRadial", label = "Arbre radial", value = FALSE),
+      checkboxInput("treeRadial", label = "Radial tree", value = FALSE),
       checkboxInput("treeSample", label = "Show samples", value = TRUE),
       selectInput(
         "treeCol",
-        label = "Couleur :",
+        label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "treeShape",
-        label = "Forme :",
+        label = "Shape : ",
         choices = c("..." = 0, sample_variables(data16S()))
       )
     )
@@ -685,10 +687,10 @@ shinyServer
   
   output$tree <- renderPlot({
     validate(
-      need(data16S(), "Merci d'importer un fichier d'abondance"),
+      need(data16S(), "Need an abundance dataset"),
       need(
         phy_tree(data16S(), errorIfNULL = FALSE),
-        "Arbre phylo invalide"
+        "Need an phylogenetic tree"
       )
     )
     p <- plot_tree(
@@ -714,12 +716,12 @@ shinyServer
   output$acpUI <- renderUI({
     validate(need(data16S(), ""))
     box(
-      title = "Paramètres",
+      title = "Setting : " ,
       width = NULL,
       status = "primary",
       selectInput(
         "acpDist",
-        label = "Distance :",
+        label = "Distance : ",
         selected = "bray",
         choices = list(
           "bray",
@@ -733,33 +735,33 @@ shinyServer
       ),
       selectInput(
         "acpMethod",
-        label = "Methode :",
+        label = "Method : ",
         selected = "MDS",
         choices = list("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")
       ),
       selectInput(
         "acpLabel",
-        label = "Label :",
+        label = "Label : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "acpCol",
-        label = "Couleur :",
+        label = "Color : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "acpShape",
-        label = "Forme :",
+        label = "Shape : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "acpEllipse",
-        label = "Ellipses :",
+        label = "Ellipses : ",
         choices = c("..." = 0, sample_variables(data16S()))
       ),
       selectInput(
         "acpRep",
-        label = "Barycentre :",
+        label = "Barycenters : ",
         choices = c("..." = 0, sample_variables(data16S()))
       )
     )
@@ -767,7 +769,7 @@ shinyServer
   
   output$acp <- renderPlot({
     validate(need(data16S(),
-                  "Merci d'importer un fichier d'abondance"))
+                  "Need an abundance dataset"))
     p <- plot_samples(
       data16S(),
       ordination = ordinate(

ui.R

@@ -3,177 +3,167 @@ shinyUI(dashboardPage(
   dashboardHeader(title = "Easy16S"),
   dashboardSidebar(
     tags$div(
-      title = "Load data for demo",
+      title = "Select dataset for demonstration",
       selectInput(
         "demo",
-        label = "Select demo data",
+        label = "Select demo dataset : ",
         choices = list("Input data" = "input",
-                       "Chaillou et al., 2015" = "food"#,
-                       # "Mach et al., 2015" = "kinetic",
-                       # "Morton et al., 2017" = "soil",
-                       # "Ravel et al., 2011" = "ravel",
-                       #"GlobalPatterns" = "GlobalPatterns",
-                       #"biorare"),
-                       selected = 1
-        )
-      ),
-      hr(width = "90%"),
-      tags$div(
-        title = "Fichier d'abondance au format BIOM produit avec FROGS avec 'FROGS BIOM to std BIOM'",
-        fileInput(
-          "fileBiom",
-          label = h4("Fichier d'abondance :"),
-          placeholder = "data.biom"
-        ),
-        radioButtons(
-          "biomFormat",
-          label = NULL,
-          inline = TRUE,
-          choices = list(`STD BIOM` = "std",
-                         `FROGS BIOM` = "frogs"),
-          selected = "std"
-        )
+                       "Chaillou et al., 2015" = "food"),
+        # "Mach et al., 2015" = "kinetic", "Morton et al., 2017" = "soil", "Ravel et al., 2011" = "ravel", "biorare" = "biorare", "GlobalPatterns" = "GlobalPatterns"
+        selected = 1
+      )
+    ),
+    hr(width = "90%"),
+    tags$div(
+      title = "Abundance BIOM file come from FROGS with 'FROGS BIOM to std BIOM', Qiime or another metagenomic tool.",
+      fileInput("fileBiom",
+                label = "Abundance BIOM file : ",
+                placeholder = "data.biom"),
+      radioButtons(
+        "biomFormat",
+        label = NULL,
+        inline = TRUE,
+        choices = list(`STD BIOM` = "std",
+                       `FROGS BIOM` = "frogs"),
+        selected = "std"
+      )
+    ),
+    tags$div(
+      style = "text-align:center",
+      title = "Resample dataset such that all samples have the same library size. \nIt's using an random sampling without replacement.",
+      checkboxInput("rareData", label = "Rarefy dataset", value = TRUE),
+      textOutput("rarefactionMin")
+    ),
+    tags$div(
+      title = "Metadata table with variables (in columns) and samples (in rows). \nMake sure you follow the exact spelling of the sample names (1st column). \nThe import of an excel table is possible but not recommended.",
+      fileInput("fileMeta",
+                label = "Metadata table : ",
+                placeholder = "data.csv")
+    ),
+    radioButtons(
+      "CSVsep",
+      label = "CSV separator : ",
+      inline = TRUE,
+      choices = list(
+        `<tab>` = "\t",
+        `,` = ",",
+        `;` = ";",
+        excel = "excel"
+      )
+    ),
+    tags$div(
+      title = "Phylogenetic tree",
+      fileInput("fileTree",
+                label = "Phylogenetic tree : ",
+                placeholder = "data.nwk")
+    )#,
+    # tags$div(
+    #   title = "Representative FASTA sequences of OTU",
+    #   fileInput(
+    #     "fileSeq",
+    #     label = "FASTA sequences : "),
+    #     placeholder = "data.fasta"
+    #   )
+    # )
+  ),