Check target + modif filtering + comment tree

Rfunctions/Data_Management.R

@@ -89,6 +89,73 @@ CheckTaxoTable <- function(taxo,counts)
   return(list(Error=Error,Warning=Warning))
 }
 
+
+
+CheckTargetModel <- function(input,target,labeled,CT)
+{
+  Error = NULL
+  HowTo = NULL
+  InterVar = input$InterestVar
+  
+  labels = rownames(target)
+  ind = which(colnames(CT)%in%labels)
+  
+  ## At least one variable selected
+  if(is.null(Error) && length(ind)<=1){
+    Error = "Less than two samples names fit with the counts table" 
+    HowTo = "Check the samples names in the target file. They must be in the first column and must correspond EXACTLY to the names in the count table."
+  }
+  ## At least one variable selected
+  if(is.null(Error) && length(InterVar)==0){
+    Error = "At least one variable must be selected for the model" 
+    HowTo = "Add at least one variable in the 'Select the variables' widget"
+  }
+  
+  
+  ## Names of samples correct ?
+  if(is.null(Error) && labeled==0){
+    Error = "The names of the samples in the target file do not fit the counts table" 
+    HowTo = "Check the samples names in the target file. They must be in the first column and must correspond EXACTLY to the names in the count table."
+    }
+  
+  ## Number of columns
+  if(is.null(Error) && ncol(target)<2){
+    Error = "The number of columns of the target file must be at least 2"
+    HowTo = "Add at least one additional variable to describe your samples"
+
+    }
+  
+  ## Number of rows
+  if(is.null(Error) && nrow(target)<=1){
+    Error = "The number of rows if the target file must be at least 2"
+    HowTo = "Add information about more than 2 samples"
+    }
+  
+  ## NA values
+  if(is.null(Error) && (any(is.na(target)) || any(target ==""))){
+    Error = "NA's or missing values are not allowed in the target file" 
+    HowTo = "Remove all the samples for which one or more variables are NA or missing"
+  }
+  
+
+  
+  ## Full rank matrix
+  if(is.null(Error) && length(InterVar)>0)
+  {
+    design = GetDesign(input)
+    testRank = CheckMatrixRank(design,target)
+    if(!testRank){
+        Error = "The model matrix is not full rank. One or more variables or interaction terms 
+        are linear combinations of the others and must be removed." 
+        HowTo = "Remove variable(s) that provide the same information, i.e, if the value of a variable is totaly determine by an other variable remove one of them."
+        }
+  }
+    
+  return(list(Error=Error,HowTo=HowTo))
+}
+
+
+
 ## Get the percentage of annotated OTU
 PercentAnnot <- function(counts,taxo)
 {
@@ -247,12 +314,10 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
     
     # Only interesting OTU
     # merged_table = merge(CT, taxo[order(rownames(CT)),], by="row.names")
-    save(CT,taxo,file="testMerge.RData")
+
     merged_table = merge(CT, taxo, by="row.names")
-    ## Why ??
     CT = merged_table[,2: (dim(CT)[2]+1)]
     taxo = merged_table[,(dim(CT)[2]+2):dim(merged_table)[2]]
-    ## ???
     
     rownames(CT) = merged_table[,1]
     rownames(taxo) = merged_table[,1]
@@ -407,7 +472,7 @@ plot_filter <- function(counts,th.samp,th.abund,type="Scatter")
   ## Initial plot for plotly
   if(type == 'Abundance' || type == 'Samples'){ 
     dataNull = data.frame(x=c(0,0),y=c(1,2),col=c("white","white"))
-    res = ggplotly(ggplot(dataNull,aes(x=x,y=y))+geom_point(aes(colour = col))+theme_bw()+ scale_color_manual(values = "white"))
+    res = ggplot(dataNull,aes(x=x,y=y))+geom_point(aes(colour = col))+theme_bw()+ scale_color_manual(values = "white")
   }
   
   res_filter = Filtered_feature(counts,th.samp,th.abund)
@@ -430,12 +495,12 @@ plot_filter <- function(counts,th.samp,th.abund,type="Scatter")
     
     ## plot the results
     gg = ggplot(df,aes(lab,y,fill=State)) + geom_bar(stat='identity') + theme_bw() +theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust = 0.5))
-    gg = gg + geom_hline( yintercept = th.abund,linetype = "longdash")
+    gg = gg + geom_hline( yintercept = th.abund,linetype = "longdash") + xlab("")
     gg = gg + scale_fill_manual(values = c('springgreen3','firebrick'))
     if(!"Kept"%in%df$State ) gg = gg + scale_fill_manual(values = 'firebrick')
     if(!"Removed"%in%df$State ) gg = gg + scale_fill_manual(values = 'springgreen3')
     
-    res = ggplotly(gg)
+    res = gg
   }
   
   if(type == 'Samples' && !is.null(th.samp) && !is.null(th.abund))
@@ -455,12 +520,12 @@ plot_filter <- function(counts,th.samp,th.abund,type="Scatter")
     ## plot the results
     
     gg = ggplot(df,aes(lab,y,fill=State)) + geom_bar(stat='identity') + theme_bw() +theme(axis.text.x = element_text(angle = 90, hjust = 1,vjust = 0.5))
-    gg = gg + geom_hline( yintercept = th.samp,linetype = "longdash")
+    gg = gg + geom_hline( yintercept = th.samp,linetype = "longdash") + xlab("")
     gg = gg + scale_fill_manual(values = c('springgreen3','firebrick'))  
     if(!"Kept"%in%df$State ) gg = gg + scale_fill_manual(values = 'firebrick')
     if(!"Removed"%in%df$State ) gg = gg + scale_fill_manual(values = 'springgreen3')
     
-    res = ggplotly(gg)
+    res = gg
     
   }
   
@@ -488,9 +553,7 @@ plot_filter <- function(counts,th.samp,th.abund,type="Scatter")
     State = df$State
     PointSize = 2
     colors_scat = list(Kept="#00CD66",Removed="#b22222")
-    print(State)
-    print(colors_scat)
-    print(head(df))
+
     res = scatterD3(x = x_var,
                      y = y_var,
                      lab = rownames(df),
@@ -532,15 +595,17 @@ plot_filter <- function(counts,th.samp,th.abund,type="Scatter")
 SelectThreshAb <- function(infile,lambda=500,graph=TRUE){
   
   rs <- rowSums(infile)
-  lambda = max(rs)
   test_Filtre <- sapply(c(min(rs):lambda),FUN=function(x) table(rs>x))
-  x <- c(min(rs):lambda)
-  reslm <- lm(test_Filtre[1,]~x)$coefficients
-  val <- which(test_Filtre[1,]>reslm[1])[1]
-  if (graph==TRUE){
-    plot(test_Filtre[1,],ylab="Nb especes avec moins de x comptages sur tous les echantillons",xlab="x")
-    abline(v=val,col="red")
-  }
-  return(val)
+  if(!is.list(test_Filtre))
+  {
+    x <- c(min(rs):lambda)
+    reslm <- lm(test_Filtre[1,]~x)$coefficients
+    val <- which(test_Filtre[1,]>reslm[1])[1]
+    if (graph==TRUE){
+      plot(test_Filtre[1,],ylab="Nb especes avec moins de x comptages sur tous les echantillons",xlab="x")
+      abline(v=val,col="red")
+    } 
+  } else val = min(rs)
+  return(max(val, min(rs)+1))
 }
 

Rfunctions/Stat_Model.R

@@ -12,20 +12,22 @@
 
 
 ## Get the possible interaction for the statistical model
-GetInteraction2 <- function(target)
+GetInteraction2 <- function(target,VarInt)
 { 
   res=c()
-  namesTarget = colnames(target)[2:ncol(target)]
-  k=1
-  for(i in 1:(length(namesTarget)-1))
-  { 
-    for(j in (i+1):length(namesTarget))
+  
+  if(length(VarInt)>=2)
+  {
+    k=1
+    for(i in 1:(length(VarInt)-1))
     { 
-      res[k] = paste(namesTarget[i],":",namesTarget[j],sep="")
-      k = k+1
+      for(j in (i+1):length(VarInt))
+      { 
+        res[k] = paste(VarInt[i],":",VarInt[j],sep="")
+        k = k+1
+      }
     }
   }
-  
   return(res)
 }
 
@@ -33,7 +35,6 @@ GetInteraction2 <- function(target)
 ## Get the dds object of DESeq2
 Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,CT_Norm)
 {
-  
   dds <- DESeqDataSetFromMatrix(countData=counts, colData=target, design=design,ignoreRank = TRUE)
   
   sizeFactors(dds) = normFactorsOTU
@@ -53,10 +54,13 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
 ## Get the design according to the input
 GetDesign <- function(input)
 {
+  design = NULL
+  Interaction = NULL
   InterVar = input$InterestVar
-  Interaction = input$Interaction2
+  if(length(InterVar)>1) Interaction = input$Interaction2
   alltmp = c(InterVar,Interaction)
-  design = as.formula(paste("~", paste0(alltmp, collapse= "+")))
+  if(length(alltmp)>0) design = as.formula(paste("~", paste0(alltmp, collapse= "+")))
+  
   return(design)
 }
 
@@ -167,6 +171,23 @@ PrintContrasts <- function (coefs, contrasts,contnames)
   
 }
 
+## Check the rank of the matrix for the statistical model.
+CheckMatrixRank <- function(design,target)
+{
+  testRank = FALSE
 
+  if(!is.null(design) && length(as.character(design))) 
+  {
+    tmp = strsplit(as.character(design)[2],"[ ]*[+][ ]*")
+    testDesign = any(unlist(tmp)%in%colnames(target))
+  }
+  
+  if(nrow(target)>=1 && ncol(target)>=2 && nrow(target)>1 && !is.null(design) && testDesign){
+    modelMatrix <- model.matrix(design, data = as.data.frame(target))
+    rk = qr(modelMatrix)$rank
+    testRank = (ncol(modelMatrix)==rk)
+  }
+    return(testRank)
+}
 
 

Rfunctions/VisuPlot.R

@@ -692,7 +692,7 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table)
   { 
     tmp = CreateTableTree(input,resDiff,CT_Norm_OTU,taxo_table,VarInt)
     
-    if(nrow(tmp$counts)>0 && !is.null(tmp$counts))
+    if(nrow(tmp$counts)>0 && !is.null(tmp$counts) && !is.null(input$TaxoTree))
     {
       merge_dat = merge(taxo_table,round(t(tmp$counts)),by="row.names")
     

server.R

 source('LoadPackages.R')
-library(plotly)
-library(treeWeightD3)
+if(!require(plotly)){
+  install.packages("plotly")
+  library(plotly)  
+}
 shinyServer(function(input, output,session) {
 
   hide(id = "loading-content", anim = TRUE, animType = "fade",time=1.5)
@@ -175,33 +177,39 @@ shinyServer(function(input, output,session) {
     normFactors = NULL
     CT_noNorm = NULL
     CT_Norm = NULL
-    #labeled= NULL
+    ChTM = NULL
     data = isolate(dataInput()$data)
     target = isolate(dataInputTarget()$target)
+    labeled= isolate(dataInputTarget()$labeled)
     taxo = isolate(input$TaxoSelect)
     
     withProgress(
     if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="..." && !is.null(target)) 
     {
       design = GetDesign(isolate(input))
-      tmp = isolate(GetCountsMerge(input,data,taxo,target,design))
-      counts = tmp$counts
+      ChTM = CheckTargetModel(input,target,labeled,data$counts)$Error
       
-      ## Filtering the counts
-      if(isolate(input$AddFilter) && !is.null(isolate(input$SliderThSamp)) && !is.null(isolate(input$SliderThAb)))
+      if(!is.null(design) && is.null(ChTM))
       {
-        ind.filter =Filtered_feature(counts,isolate(input$SliderThSamp),isolate(input$SliderThAb))$ind
-        counts = counts[-ind.filter,]
+        tmp = isolate(GetCountsMerge(input,data,taxo,target,design))
+        counts = tmp$counts
+        
+        ## Filtering the counts
+        if(isolate(input$AddFilter) && !is.null(isolate(input$SliderThSamp)) && !is.null(isolate(input$SliderThAb)))
+        {
+          ind.filter =Filtered_feature(counts,isolate(input$SliderThSamp),isolate(input$SliderThAb))$ind
+          counts = counts[-ind.filter,]
+        }
+        
+        CheckTarget = tmp$CheckTarget
+        #target = tmp$target
+        #labeled = tmp$labeled
+        normFactors = tmp$normFactors
+        
+        ## OTU table, norm and no norm
+        CT_noNorm = tmp$CT_noNorm
+        CT_Norm = tmp$CT_Norm
       }
-      
-      CheckTarget = tmp$CheckTarget
-      #target = tmp$target
-      #labeled = tmp$labeled
-      normFactors = tmp$normFactors
-      
-      ## OTU table, norm and no norm
-      CT_noNorm = tmp$CT_noNorm
-      CT_Norm = tmp$CT_Norm
     }
     ,message="Merging the counts ...")
     return(list(counts=counts,CheckTarget=CheckTarget,normFactors=normFactors,CT_noNorm=CT_noNorm, CT_Norm=CT_Norm))
@@ -277,7 +285,8 @@ shinyServer(function(input, output,session) {
     res = NULL
     counts = isolate(dataMergeCounts()$counts)
     tot = rowSums(counts)
-    tmp = SelectThreshAb(counts,lambda=max(round(sum(counts)/nrow(counts)*0.05),min(tot)+1),graph=FALSE)
+    save(counts,tot,file="testFilter.RData")
+    withProgress({tmp = SelectThreshAb(counts,lambda=max(round(sum(counts)/nrow(counts)*0.05),min(tot)+1),graph=FALSE)},message="Loading...")
     
     res = sliderInput("SliderThAb","Threshold on the total abundance (in log)",min=0,max=round(max(log(tot+1)),1),value = log(tmp+1))
     return(res)
@@ -305,14 +314,14 @@ shinyServer(function(input, output,session) {
   
   # plot_filter(counts,th.samp,th.abund,type="Scatter")
   
-  output$Plot_ThAb <- renderPlotly({
+  output$Plot_ThAb <- renderPlot({
     counts = dataMergeCounts()$counts
     ## output of plot_filter is ggplot class
     plot_filter(counts,input$SliderThSamp,input$SliderThAb,type="Abundance")
     
   })
     
-  output$Plot_ThSamp <- renderPlotly({
+  output$Plot_ThSamp <- renderPlot({
     counts = dataMergeCounts()$counts
     ## output of plot_filter is ggplot class
     plot_filter(counts,input$SliderThSamp,input$SliderThAb,type="Samples")
@@ -480,17 +489,17 @@ shinyServer(function(input, output,session) {
     ind = which(rownames(data)%in%colnames(counts))
     data = as.data.frame(data[ind,])
     colnames(data) = names
-    
     ## Replace "-" by "."
-    ind_num = which(sapply(as.data.frame(data[,-1]),is.numeric)) + 1
-    if(length(ind_num)>0){
-      data_tmp =cbind( as.data.frame(apply(as.data.frame(data[,-ind_num]),2,gsub,pattern = "-",replacement = ".")),data[,ind_num])
-      colnames(data_tmp) = c(colnames(data)[-ind_num],colnames(data)[ind_num])
-      data = data_tmp
+    if(ncol(data)>1 && nrow(data)>1){
+      ind_num = which(sapply(as.data.frame(data[,-1]),is.numeric)) + 1
+      if(length(ind_num)>0){
+        data_tmp =cbind( as.data.frame(apply(as.data.frame(data[,-ind_num]),2,gsub,pattern = "-",replacement = ".")),data[,ind_num])
+        colnames(data_tmp) = c(colnames(data)[-ind_num],colnames(data)[ind_num])
+        data = data_tmp
+      }
+      if(length(ind_num)==0){data = as.data.frame(apply(data,2,gsub,pattern = "-",replacement = "."))}
     }
-    if(length(ind_num)==0){data = as.data.frame(apply(data,2,gsub,pattern = "-",replacement = "."))}
-    
-    target = data
+    target = as.data.frame(data)
     
     # target = as.data.frame(apply(target,2,gsub,pattern = "-",replacement = "."))
     
@@ -522,18 +531,20 @@ shinyServer(function(input, output,session) {
     
   })
   
-  
   ## Interactions
   output$SelectInteraction2 <- renderUI({
     
     target = dataInputTarget()$target
-    
-    if(!is.null(target)) 
+    VarInt = input$InterestVar
+    res = NULL
+    if(!is.null(target) && length(input$InterestVar)>1) 
     {
-      Interac = GetInteraction2(target)
-      selectInput("Interaction2",h6(strong("Add interactions")),Interac,selected=NULL,multiple=TRUE)
+      Interac = GetInteraction2(target,VarInt)
+      res = selectInput("Interaction2",h6(strong("Add interactions")),Interac,selected=NULL,multiple=TRUE)
     }
+    if(length(input$InterestVar)==1) res = NULL
     
+    return(res)
   })
 
 
@@ -1134,6 +1145,65 @@ shinyServer(function(input, output,session) {
   })
   
   
+  # Infobox model/target
+#   output$InfoModel<- renderInfoBox({
+#     res = infoBox(h6(strong("Target file and variables")), 
+#                   subtitle = h6(strong("Your target file must contain at least 2 columns and 2 rows. NA's values are not allowed and the variables must not be collinear.")), 
+#                   icon = icon("book"),color = "green",width=NULL,fill=TRUE)
+#     
+#     target = dataInputTarget()$target
+#     taxo = input$TaxoSelect
+#     ChTM = NULL
+#     
+#     ## Return NULL if there is no error
+#     if(!is.null(target)) ChTM = CheckTargetModel(input,target)
+#   
+#     if(!is.null(ChTM)) res = infoBox(h6(strong("Error")), subtitle = h6(ChTM), icon = icon("thumbs-o-down"),color = "red",width=NULL,fill=TRUE)
+#     
+#     return(res)
+#     
+#     })
+  
+  output$InfoModel<- renderUI({
+    
+    CT = dataInput()$data$counts
+    target = dataInputTarget()$target
+    labeled = dataInputTarget()$labeled
+    taxo = input$TaxoSelect
+    ChTM = NULL
+    
+    ## Return NULL if there is no error
+    if(!is.null(target)) ChTM = CheckTargetModel(input,target,labeled,CT)
+    
+    if(!is.null(ChTM$Error)) {   
+      box(title = "Error", status = "danger",width = 6,
+          h6(strong(ChTM$Error)),
+          footer = em("Reminder: Your target file must contain at least 2 columns and 2 rows. NA's values are not allowed and the variables must not be collinear.")
+      )
+    }
+    
+  })
+  
+  output$InfoModelHowTo<- renderUI({
+    
+    CT = dataInput()$data$counts
+    target = dataInputTarget()$target
+    labeled = dataInputTarget()$labeled
+    taxo = input$TaxoSelect
+    ChTM = NULL
+    
+    ## Return NULL if there is no error
+    if(!is.null(target)) ChTM = CheckTargetModel(input,target,labeled,CT)
+    
+    if(!is.null(ChTM$HowTo)) {   
+      box(title = "How To", status = "success",width = 6,
+          h6(strong(ChTM$HowTo))
+      )
+    }
+    
+  })
+  
+  
   
   #####################################################
   ##
@@ -1503,9 +1573,18 @@ shinyServer(function(input, output,session) {
   output$RunButton <- renderUI({
     
     res = NULL
+    ChTM = "Error"
     target = dataInputTarget()$target
+    labeled = dataInputTarget()$labeled
+    CT = dataInput()$data$counts
     taxo = input$TaxoSelect
-    if(!is.null(target) && taxo!="...") res = actionButton("RunDESeq",strong("Run analysis"),icon = icon("caret-right"))
+    VarInt = input$InterestVar
+    
+    ## Return NULL if there is no error
+    if(!is.null(target) && length(VarInt)>=1) ChTM = CheckTargetModel(input,target,labeled,CT)$Error
+
+    if(!is.null(target) && taxo!="..." && is.null(ChTM) && length(VarInt)>=1) res = actionButton("RunDESeq",strong("Run analysis"),icon = icon("caret-right"))
+    
     return(res)
   })
   
@@ -2017,36 +2096,29 @@ shinyServer(function(input, output,session) {
   observe({
     
     input$TaxoSelect
-    testRank = FALSE
     counts = dataMergeCounts()$counts
-    InterVar = input$InterestVar
-    
-
-    if(length(InterVar)>0)
-    {
-      design = GetDesign(input)
-      target = dataInputTarget()$target
-      modelMatrix <- model.matrix(design, data = as.data.frame(target))
-      rk = qr(modelMatrix)$rank
-      testRank = (ncol(modelMatrix)==rk)
-    }
-    
+    ChTM = ""
+    CT = dataInput()$data$counts
+    target = dataInputTarget()$target
+    labeled= dataInputTarget()$labeled
+    ChTM = CheckTargetModel(input,target,labeled,CT)$Error
     
-    if(input$AddFilter && !is.null(input$SliderThSamp) && !is.null(input$SliderThAb))
+    if(input$AddFilter && !is.null(input$SliderThSamp) && !is.null(input$SliderThAb) && is.null(ChTM))
     {
       ind.filter =Filtered_feature(counts,input$SliderThSamp,input$SliderThAb)$ind
       counts = counts[-ind.filter,]
     }
 
+    
     if (!is.null(counts)){
       if (nrow(counts)>=2){
         shinyjs::enable("RunDESeq")
       }
-      if (nrow(counts)<2 || !testRank) {
+      if (nrow(counts)<2) {
         shinyjs::disable("RunDESeq")
       }
     } 
-    if (is.null(counts) || !testRank) {
+    if (is.null(counts) ) {
       shinyjs::disable("RunDESeq")
     }
 

ui.R

@@ -6,7 +6,7 @@ if (!require(devtools)) {
   library(devtools)
 }
 if(!require(treeWeightD3)){
-  devtools::install_git('https://gitlab.pasteur.fr/plechat/treeWeightD3')
+  devtools::install_git('https://gitlab.pasteur.fr/plechat/treeWeightD3.git')
   library(treeWeightD3)
 }
 if (!require(scatterD3)) {
@@ -25,7 +25,11 @@ if(!require(shinyjs)){
   install.packages("shinyjs")
   library(shinyjs)  
 }
-library(plotly)
+if(!require(plotly)){
+  install.packages("plotly")
+  library(plotly)  
+}
+
 function(request) {
 sidebar <- dashboardSidebar(
   useShinyjs(),
@@ -309,10 +313,13 @@ body <- dashboardBody(
                   ),
                   fluidRow( 
                     column(width=6,uiOutput("SelectInterestVar")),
-                    column(width=6,uiOutput("SelectInteraction2")),
+                    column(width=6,uiOutput("SelectInteraction2"))
+                  ),
+                  fluidRow( 
                     column(width=6,uiOutput("RunButton"))
                   )
                 ),
+                fluidRow(uiOutput("InfoModel"),uiOutput("InfoModelHowTo")),
                 uiOutput("BoxTarget"),
                 uiOutput("BoxCountsMerge")
               ),
@@ -372,11 +379,11 @@ body <- dashboardBody(
                                     fluidRow(
                                       conditionalPanel(condition="input.AddFilter",
                                               column(width=6, 
-                                                     plotlyOutput("Plot_ThSamp"),
+                                                     plotOutput("Plot_ThSamp"),
                                                      column(width=10,uiOutput("ThSamp"),offset = 1)
                                                      ),
                                               column(width=6,
-                                                     plotlyOutput("Plot_ThAb"),
+                                                     plotOutput("Plot_ThAb"),
                                                      column(width=10,uiOutput("ThAb"),offset = 1)
                                                      ),
                                               column(width=12,
@@ -589,7 +596,8 @@ body <- dashboardBody(
 
             column(width=3,
               box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
-                  selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Tree"="Tree","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "Barplot")
+                  # selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Tree"="Tree","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "Tree")
+                  selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "Barplot")
               ),