Debug comparison plot in the case where a contrast is empty

Rfunctions/CompPlot.R

@@ -46,7 +46,7 @@ Plot_Visu_Heatmap_FC <- function(input, BaseContrast, resDiff, ContrastListDebou
 ##############################
 ##      P VALUE DENSITY PLOT
 ##############################
-Plot_pValue_Density <- function(input, BaseContrast, resDiff, ContrastListDebounce, alphaVal){
+Plot_pValue_Density <- function(input, BaseContrast, resDiff, ContrastListDebounce, alphaVal, InputpValueDensityfocus){
   res = NULL
   #SelContrast = input$ContrastList_table_FC
   SelContrast = ContrastListDebounce()
@@ -64,8 +64,10 @@ Plot_pValue_Density <- function(input, BaseContrast, resDiff, ContrastListDeboun
     data <- rbind(data, data_cont)
   }
   data$contrast <- factor(data$contrast, levels = SelContrast)
-                                                                                                                          # uncomment to zoom (X axis between 0 and input$alphaVal)                               (use "+ xlim(0,as.numeric(alphaVal))" instead, to redraw geom_density with only data under threshold)
-  p <- ggplot(data, aes(x = padj, color = contrast, fill = contrast)) + geom_density(alpha = input$fillOpacity, size = input$lineWidth) + theme_minimal() #+ coord_cartesian(xlim = c(0,as.numeric(alphaVal)))
+  p <- ggplot(data, aes(x = padj, color = contrast, fill = contrast)) + theme_minimal()
+  InputpValueDensityfocus() # for reactivity
+  if(isolate(input$adaptBWtoFocus)){p <- p + geom_density(alpha = input$fillOpacity, size = input$lineWidth, adjust = as.numeric(alphaVal), n = 2 ^ (input$numberPoints))}else{p <- p + geom_density(alpha = input$fillOpacity, size = input$lineWidth, adjust = 1, n = 2 ^ (input$numberPoints))}
+  if(isolate(input$focusUnderThreshold)){p <- p + coord_cartesian(xlim = c(0,as.numeric(alphaVal)))}
   p <- p + theme(axis.title = element_text(size = input$FontSizepValueDensity), 
                  axis.text = element_text(size = input$FontSizepValueDensity),
                  legend.title = element_text(size = input$FontSizepValueDensity),
@@ -130,8 +132,6 @@ Plot_Comp_Logit <- function(input, BaseContrast, resDiff, SelectTaxoPlotCompDebo
                         ylab = paste("logit p value", input$Contrast2),
                         hover_opacity = 1,
                         tooltip_text = row.names(padj),
-                        # xlim = xlimits,
-                        # ylim = ylimits,
                         lines = if (input$showSignifThresholdsLogitPlot) {
                           if(input$showDiagonal){
                             data.frame(
@@ -180,8 +180,6 @@ Plot_Comp_Logit <- function(input, BaseContrast, resDiff, SelectTaxoPlotCompDebo
                         # dom_id_reset_zoom = "scatterD3-reset-zoomLogit",
                         # dom_id_svg_export = "scatterD3-svg-exportLogit",
                         # menu = FALSE,
-                        # height = input$heightVolcanoPlot,
-                        # width=if(input$modifwidthVolcano){input$widthVolcanoPlot},
                         # disable_wheel = TRUE
                         )
       }
@@ -219,13 +217,20 @@ Plot_Comp_Logit <- function(input, BaseContrast, resDiff, SelectTaxoPlotCompDebo
 ##############################
 Plot_Visu_Venn <- function(input,BaseContrast,resDiff, ContrastListVennDebounce, export=FALSE){
   res = NULL
+  contrasts_without_diff = NULL
   #SelContrast = input$ContrastList_table_FCVenn
   SelContrast = ContrastListVennDebounce()
   if(length(SelContrast)>=2 & length(SelContrast)<=4){
-  data = GetData_venn(input,SelContrast,BaseContrast,resDiff)$res
+    gotData = GetData_venn(input,SelContrast,BaseContrast,resDiff)
+    
+    data2 = gotData$df.tot
+    if(length(SelContrast) - length(colnames(data2[sapply(data2,function(x) all(is.na(x)))])) < 2){contrasts_without_diff = colnames(data2[sapply(data2,function(x) all(is.na(x)))])
+    }
+    else{
+  data = gotData$res
   res = venn_tooltip(d3vennR(data=data))
-  }
-  return(res)
+  }}
+  return(list(res = res, contrasts_without_diff=contrasts_without_diff))
 }
 
 ##############################
@@ -234,10 +239,16 @@ Plot_Visu_Venn <- function(input,BaseContrast,resDiff, ContrastListVennDebounce,
 Plot_UpSet <- function(input,BaseContrast, resDiff, ContrastListDebounce, export=FALSE){
   plot = NULL
   df = NULL
+  contrasts_without_diff = NULL
   #SelContrast = input$ContrastList_table_FC
   SelContrast = ContrastListDebounce()
   if(length(SelContrast)>=2){
-    data = GetData_venn(input,SelContrast,BaseContrast,resDiff)$df.tot
+    gotData = GetData_venn(input,SelContrast,BaseContrast,resDiff)
+    data = gotData$df.tot
+    
+    if(length(SelContrast) - length(colnames(data[sapply(data,function(x) all(is.na(x)))])) < 2){contrasts_without_diff = colnames(data[sapply(data,function(x) all(is.na(x)))])
+    }
+    else{
     listInput <- list()
     n <- ncol(data)
     for(i in 1:n){
@@ -274,19 +285,27 @@ Plot_UpSet <- function(input,BaseContrast, resDiff, ContrastListDebounce, export
     maxRow = max(apply(df,2,FUN=function(x) length(which(!is.na(x)))))
     df = df[1:max(maxRow,1),]
     df = df[,which(apply(!is.na(df),2,any))]
-  }
-  return(list(plot=plot,table=df))
+  }}
+  return(list(plot=plot,table=df, contrasts_without_diff=contrasts_without_diff))
 }
 
 
 ##############################
-##   MULTIPLE VENN COMPAIR
+##   Contrasts comparison
 ##############################
 Plot_MultipleVenn <- function(input,BaseContrast, resDiff, ContrastListDebounce){
   plot = NULL
+  contrasts_without_diff = NULL
   SelContrast = ContrastListDebounce()
   if(length(SelContrast)>=2){
-  data = GetData_venn(input,SelContrast,BaseContrast,resDiff)$res_multiple_venn
+  gotData = GetData_venn(input,SelContrast,BaseContrast,resDiff)
+  
+  data2 = gotData$df.tot
+  if(length(SelContrast) - length(colnames(data2[sapply(data2,function(x) all(is.na(x)))])) < 2){contrasts_without_diff = colnames(data2[sapply(data2,function(x) all(is.na(x)))])
+  }
+  else{
+  
+  data = gotData$res_multiple_venn
 
   plot <- ggplot(data,aes(x=x,y=y)) + geom_point() + theme_bw() + 
           geom_label_repel(aes(label=name), size = input$labelSizemultipleVenn) + xlim(c(0,1)) + ylim(c(0,1)) + 
@@ -294,8 +313,8 @@ Plot_MultipleVenn <- function(input,BaseContrast, resDiff, ContrastListDebounce)
           ylab(bquote(Contrast1 *intersect(Contrast2) ~ "/ Contrast2"))
   plot <- plot + theme(axis.title = element_text(size = input$FontSizeMultipleVenn), 
                  axis.text = element_text(size = input$FontSizeMultipleVenn - 2))
-  }
-  return(plot)
+  }}
+  return(list(plot = plot, contrasts_without_diff=contrasts_without_diff))
 }
 
 
@@ -342,20 +361,17 @@ Get_log2FC_padj <-function(input,BaseContrast,resDiff, info = NULL)
                                 independentFiltering=input$IndFiltering,alpha=alpha)
     }
     log2FC = as.matrix(round(result[[SelContrast[1]]][, "log2FoldChange"], 3))
-    #padj = as.matrix(round(result[[SelContrast[1]]][, "padj"], 3))
     padj = as.matrix((result[[SelContrast[1]]][, "padj"]))
     if(nbCont>1)
     {
       for(i in 2:nbCont)
       {
         log2FC = cbind(log2FC,round(result[[SelContrast[i]]][, "log2FoldChange"], 3))
-        #padj = cbind(padj,round(result[[SelContrast[i]]][, "padj"], 7))
         padj = cbind(padj,(result[[SelContrast[i]]][, "padj"]))
       }
-    }#  
-      colnames(log2FC) = names(result)
-      colnames(padj) = names(result)
-    #}
+    }  
+    colnames(log2FC) = names(result)
+    colnames(padj) = names(result)
     
     rownames(log2FC) = rownames(result[[SelContrast[1]]])
     rownames(padj) = rownames(result[[SelContrast[1]]])
@@ -429,7 +445,7 @@ venn_tooltip <- function(venn){
   }
 
 
-## Transform the data for the venn diagram
+## Transform the data for the venn diagram and the "contrasts comparison"
 GetData_venn <-function(input,SelContrast,BaseContrast,resDiff)
 {
   res = list()
@@ -506,7 +522,7 @@ GetData_venn <-function(input,SelContrast,BaseContrast,resDiff)
                         }
                     }
           }
-          # For 'Multiple Venn Compair'
+          # For 'Contrasts comparison'
           if(i!=j) {
             if (is.null(res_multiple_venn))
               {res_multiple_venn <- data.frame(name = c(rownames_multiple_venn, paste(names.df[i],names.df[j], sep = " vs ")), 

Rfunctions/TablesPlot.R

@@ -154,13 +154,6 @@ Volcano_Plot <- function(input, data, export = FALSE) {
       } else{
         ""
       })
-  # labels <-
-  #   sapply(names, function(name)
-  #     if (is.element(name, points_to_label)) {
-  #       name
-  #     } else{
-  #       ""
-  #     })
   if(!export){
   plot <-
     scatterD3(

Rfunctions/VisuPlot.R

@@ -2,9 +2,9 @@
 #@ visualisation plots of SHAMAN
 
 
-###########################
-##        Barplot
-###########################
+##                       ##
+##        Barplot ####
+##                       ##
 
 Plot_Visu_Barplot <- function(input,resDiff)
 {
@@ -76,9 +76,9 @@ Plot_Visu_Barplot <- function(input,resDiff)
    
     
     
-    ##################################
+    ##                                 ##
     ## Same plot in ggplot2 for export
-    ##################################
+    ##                                 ##
     
     tax.colors=rep(c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78", "#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b",
                      "#c49c94","#e377c2","#f7b6d2","#7f7f7f", "#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"),ceiling(nbKept/20))
@@ -99,9 +99,9 @@ Plot_Visu_Barplot <- function(input,resDiff)
 
 
 
-##############################
-##          HEATMAP
-##############################
+##                       ##
+##          HEATMAP ####
+##                       ##
 Plot_Visu_Heatmap <- function(input,resDiff,export=FALSE){
   
   VarInt = input$VisuVarInt
@@ -144,9 +144,9 @@ Plot_Visu_Heatmap <- function(input,resDiff,export=FALSE){
 
 
 
-##############################
-##          BOXPLOTS
-##############################
+##                       ##
+##          BOXPLOTS ####
+##                       ##
 Plot_Visu_Boxplot <- function(input,resDiff,alpha=0.7){
   
   gg = NULL
@@ -219,9 +219,9 @@ Plot_Visu_Boxplot <- function(input,resDiff,alpha=0.7){
   return(gg)
 }
 
-##############################
-##          KRONA
-##############################
+##                       ##
+##          KRONA ####
+##                       ##
 Plot_Visu_Krona <- function(input,resDiff,CT_OTU,taxo_table){
   
   res = NULL
@@ -256,9 +256,9 @@ Plot_Visu_Krona <- function(input,resDiff,CT_OTU,taxo_table){
   return(res)
 }
 
-##############################
-##      Phylo PLOT
-##############################
+##                       ##
+##      Phylo PLOT ####
+##                       ##
 Plot_Visu_Phylotree = function(input, resDiff, CT_OTU, taxo_table, treeseq){
   res = NULL
   VarInt = input$VisuVarInt
@@ -296,9 +296,9 @@ Plot_Visu_Phylotree = function(input, resDiff, CT_OTU, taxo_table, treeseq){
 }
   
 
-##############################
-##      SCATTER PLOT
-##############################
+##                       ##
+##      SCATTER PLOT ####
+##                       ##
 Plot_Visu_Scatterplot<- function(input,resDiff,export=FALSE,lmEst = FALSE,CorEst=FALSE){
   
   plot = NULL
@@ -410,9 +410,9 @@ Plot_Visu_Scatterplot<- function(input,resDiff,export=FALSE,lmEst = FALSE,CorEst
 
 
 
-##############################
-##      Diversity
-##############################
+##                       ##
+##      Diversity ####
+##                       ##
 Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE){
   gg = NULL
   dataTmp = NULL
@@ -528,9 +528,9 @@ Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE){
 }
 
 
-##############################
-##       RAREFACTION
-##############################
+##                       ##
+##       RAREFACTION ####
+##                       ##
 Plot_Visu_Rarefaction <- function(input,resDiff,xlim,ylim,ylab="Species"){
   
   PlotRare = NULL
@@ -558,11 +558,11 @@ Plot_Visu_Rarefaction <- function(input,resDiff,xlim,ylim,ylab="Species"){
 
 
 
-##############################################################
+##                                      ##
 ##
-##          Useful functions
+##          Useful functions ####
 ##
-##############################################################
+##                                      ##
 
 ## Get the non-zero taxo by sample  
 TaxoNumber <-  function (x, groups, mar = 1) 
@@ -795,9 +795,9 @@ CreateTableTree <- function(input,resDiff,CT_Norm_OTU,taxo_table,VarInt,ind_taxo
 
 
 
-###########################
+##                       ##
 ##        Tree
-###########################
+##                       ##
 
 ## The count matrix must be given at the leaf level.
 
@@ -833,9 +833,9 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table)
   return(res)
 }
 
-#############################
+##                       ##
 ##      NETWORK
-#############################
+##                       ##
 
 Plot_network <- function(input,resDiff,availableTaxo, ind_taxo, qualiVariable, export = FALSE){
   plot = NULL
@@ -864,19 +864,19 @@ Plot_network <- function(input,resDiff,availableTaxo, ind_taxo, qualiVariable, e
     adjacency <- matrix(mapply(function(a,b) {mapply(function(x,y){x*y}, x=a, y=b)}, a=pval_bool, b=cor_sgn), nrow = n)
     rownames(adjacency) <- colnames(countsMatrix)
     colnames(adjacency) <- colnames(countsMatrix)
-    # ### Remove rows and columns with only NA
+    # ### Remove rows and columns with only NA        # this way, elements with the same count in all sample (often 0 in this case) will not appear
     # adjacency <- adjacency[apply(adjacency, 1, function(y) !all(is.na(y))),]
     # adjacency <- t(adjacency)
     # adjacency <- adjacency[apply(adjacency, 1, function(y) !all(is.na(y))),]
     # adjacency <- t(adjacency)
     
-    ### Replace NA by zeros (ie "no correlation")
+    ### Replace NA by zeros (ie "no correlation")     # this way, those elements will appear as single nodes
     adjacency[is.na(adjacency)] <- 0
     
     adjacency <- adjacency[,ind_taxo]
     adjacency <- adjacency[ind_taxo,]
     
-    igraphGraph <- graph_from_adjacency_matrix(adjacency, diag = FALSE, mode = "upper" , weighted = TRUE) # "upper" for adjusted p-value, lower for p-value not adjusted
+    igraphGraph <- graph_from_adjacency_matrix(adjacency, diag = FALSE, mode = "upper" , weighted = TRUE) # mode = "upper" for adjusted p-value, mode = "lower" for p-value not adjusted
     
     list_to_label <- isolate(input$ToLabelNetwork)
     dataVN <- toVisNetworkData(igraphGraph)
@@ -898,7 +898,7 @@ Plot_network <- function(input,resDiff,availableTaxo, ind_taxo, qualiVariable, e
     
     plot <- visNetwork(nodes = dataVN$nodes, edges = dataVN$edges)
     plot <- visIgraphLayout(plot, layout = "layout_nicely", physics = FALSE, smooth = FALSE)
-    plot <- visNodes(plot, size = 20) #, scaling = list(label = list(min = 30, max = 30, maxVisible = 30)))
+    plot <- visNodes(plot, size = 20)
     plot <- visEdges(plot, width = 1)
     plot <- visOptions(plot, width = if(isolate(input$modifwidthVisu)){isolate(input$widthVisu)}, height = isolate(input$heightVisu), autoResize = FALSE)
     #plot <- visLegend(plot, addEdges = data.frame(color = c("red", "blue"), label = c("Positive correlation","Negative correlation")))

server.R

@@ -2,11 +2,11 @@ shinyServer(function(input, output,session) {
   
   hide(id = "loading-content", anim = TRUE, animType = "fade",time=1.5)
   hide(id = "loading-content-bar", anim = TRUE, animType = "fade",time=1.5)
-  #####################################################
+  ###                                               ###
   ##
-  ##                    LOAD FILES
+  ####                    LOAD FILES ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   
@@ -518,11 +518,11 @@ shinyServer(function(input, output,session) {
     ## output of plot_filter is ggplot class
     plot_filter(counts,input$SliderThSamp,input$SliderThAb,type="Scatter")
   })
-  #####################################################
+  ###                                               ###
   ##
-  ##                DYNAMIC MENU
+  ##                DYNAMIC MENU ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   
@@ -556,11 +556,11 @@ shinyServer(function(input, output,session) {
   
   
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                DATA TABLE
+  ##                DATA TABLE ####
   ##
-  #####################################################
+  ###                                               ###
   
   ## Counts Table
   output$DataCounts <- DT::renderDataTable(
@@ -715,11 +715,11 @@ shinyServer(function(input, output,session) {
     return(res)
   })
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                TARGET FILE
+  ##                TARGET FILE ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   ## Load target file
@@ -784,11 +784,11 @@ shinyServer(function(input, output,session) {
   
   
   
-  #############################################################
+  ###                                               ###
   ##
-  ##                        MASQUE
+  ##                        MASQUE ####
   ##
-  #############################################################
+  ###                                               ###
   
   
   
@@ -1160,7 +1160,7 @@ shinyServer(function(input, output,session) {
     htmltools::HTML('<img src="icons/underhill.png" alt="dna" style="width:80px;height:80px;">')
   )
   
-  #####################################
+  ###                                               ###
   
   
   
@@ -1935,6 +1935,24 @@ shinyServer(function(input, output,session) {
     return(res)
   })
   
+  ## Run button
+  output$RunButton <- renderUI({
+    
+    res = NULL
+    ChTM = "Error"
+    target = values$TargetWorking
+    labeled = values$labeled
+    CT = dataInput()$data$counts
+    taxo = input$TaxoSelect
+    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)
+  })
   
   ## Var for normalization
   output$SelectVarNorm <- renderUI({
@@ -2081,11 +2099,11 @@ shinyServer(function(input, output,session) {
   
   
   
-  #####################################################
+  ###                                               ###
   ##
-  ##            DEFINE CONTRAST
+  ##            DEFINE CONTRAST ####
   ##
-  #####################################################
+  ###                                               ###
   
   output$contrastMat <- renderUI({
     
@@ -2529,11 +2547,11 @@ shinyServer(function(input, output,session) {
   }, priority=1)
   
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                DESEQ2 run
+  ##                DESEQ2 run ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   
@@ -2575,11 +2593,11 @@ shinyServer(function(input, output,session) {
   })
   
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                Taxonomy
+  ##                Taxonomy ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   # Infobox Contrast
@@ -2729,11 +2747,11 @@ shinyServer(function(input, output,session) {
   
   
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                Diagnostic plots
+  ##                DIAGNOSTIC PLOTS ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   
@@ -2955,11 +2973,11 @@ shinyServer(function(input, output,session) {
   
   
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                EXPORT DIAG GRAPH
+  ##                EXPORT DIAG GRAPH ####
   ##
-  #####################################################
+  ###                                               ###
   
   #### Export Diag
   output$exportdiag <- downloadHandler(
@@ -2977,11 +2995,11 @@ shinyServer(function(input, output,session) {
     }
   )
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                EXPORT VISU GRAPH
+  ##                EXPORT VISU GRAPH ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   #### Export Visu
@@ -3025,16 +3043,16 @@ shinyServer(function(input, output,session) {
       if(is.na(filesize)){filesize=0}
       
       if(input$PlotVisuSelectComp=="Venn"){ 
-        if(filesize!=0) print(Plot_Visu_Venn(input,BaseContrast,ResDiffAnal(),ContrastListVennDebounce, export=TRUE))
+        if(filesize!=0) print(Plot_Visu_Venn(input,BaseContrast,ResDiffAnal(),ContrastListVennDebounce, export=TRUE)$res)
       }
       if(input$PlotVisuSelectComp=="Heatmap_comp"){
         if(filesize!=0) Plot_Visu_Heatmap_FC(input,BaseContrast,ResDiffAnal(),ContrastListDebounce, SelectTaxoPlotCompDebounce, export=TRUE)
       }
       if(input$PlotVisuSelectComp=="pValueDensity"){
-        if(filesize!=0) print(Plot_pValue_Density(input, BaseContrast, ResDiffAnal(), ContrastListDebounce, input$AlphaVal))
+        if(filesize!=0) print(Plot_pValue_Density(input, BaseContrast, ResDiffAnal(), ContrastListDebounce, input$AlphaVal, InputpValueDensityfocus))
       }
       if(input$PlotVisuSelectComp=="multipleVenn"){
-        if(filesize!=0) print(Plot_MultipleVenn(input, BaseContrast, ResDiffAnal(), ContrastListDebounce))
+        if(filesize!=0) print(Plot_MultipleVenn(input, BaseContrast, ResDiffAnal(), ContrastListDebounce)$plot)
       }
       if(input$PlotVisuSelectComp=="UpSet"){
         if(filesize!=0) print(Plot_UpSet(input, BaseContrast, ResDiffAnal(), ContrastListDebounce)$plot)
@@ -3067,11 +3085,11 @@ shinyServer(function(input, output,session) {
   )
   
   
-  #####################################################
+  ###                                               ###
   ##
-  ##                DIFF TABLES
+  ##                DIFF TABLES ####
   ##
-  #####################################################
+  ###                                               ###
   
   
   #   output$ContrastListTable <- renderUI({
@@ -3215,29 +3233,12 @@ shinyServer(function(input, output,session) {
     }
   })
   
-  # output$TabBoxTablesPlot <- renderUI({
-  #   tabBox(
-  #     id = "tabBoxPlotTables",
-  #     width = NULL,
-  #     selected = "Bar chart",
-  #     tabPanel(
-  #       "Bar chart",
-  #       amChartsOutput("BarChartTables", height = input$heightBarChartTables)
-  #     ),
-  #     tabPanel(
-  #       "Volcano plot",
-  #       scatterD3Output("VolcanoPlot", height = input$heightVolcanoPlot, width = input$widthVolcanoPlot)
-  #     )
-  #   )
-  # })
-  
   output$BarChartContainer <- renderUI({
     fluidPage(amChartsOutput("BarChartTables", height = input$heightBarChartTables))
   })
   
   output$VolcanoPlotContainer <- renderUI({
-
-    fluidPage(scatterD3Output("VolcanoPlot", height = input$heightVolcanoPlot + 10, width=ifelse(input$modifwidthVolcano,input$widthVolcanoPlot,"100%")))#width = input$widthVolcanoPlot + 10))
+    fluidPage(scatterD3Output("VolcanoPlot", height = input$heightVolcanoPlot + 10, width=ifelse(input$modifwidthVolcano,input$widthVolcanoPlot,"100%")))
   })
   
   output$BarChartTables <- renderAmCharts({
@@ -3262,10 +3263,9 @@ shinyServer(function(input, output,session) {
       withProgress(message = "Loading...", Volcano_Plot(input, data))