Modif VarInt Visu + correction density + correction clustering

internal.R

@@ -365,12 +365,12 @@ CheckCountsTable <- function(counts)
     
     if(type=="hori") 
     { 
-      par(cex=input$cexTitleDiag,mar = c(0.3,2,0.3,2))
+      par(cex=input$cexTitleDiag,mar=c(6,6,4,5))
       res = plot(dend, main = "Cluster dendrogram",xlab = paste(input$DistClust,"distance, Ward criterion",sep=" "),cex=input$cexLabelDiag)
     }  
     if(type!="hori")
     {
-      par(cex=input$cexTitleDiag,mar = c(0.3,2,0.3,2))
+      par(cex=input$cexTitleDiag,mar=c(6,6,4,5))
       res = circlize_dendrogram(dend, labels_track_height = 0.2, dend_track_height = .3, main = "Cluster dendrogram",xlab = paste(input$DistClust,"distance, Ward criterion",sep=" "))
     }
     return(res)
@@ -475,19 +475,19 @@ CheckCountsTable <- function(counts)
     par(cex=input$cexTitleDiag,mar=c(8,5,4,5))
     plot(density(log2(counts[, 1] + 1)), las = 1, lwd = 2, main = "Density of counts distribution", 
          xlab = expression(log[2] ~ (raw ~ count + 1)), 
-         ylim = c(0, max(apply(counts, 2, function(x) {max(density(log2(x + 1))$y)})) * 1.05), 
+         ylim = c(-0.2, max(apply(counts, 2, function(x) {max(density(log2(x + 1))$y)})) * 1.05), 
          lty = if (ncol1) {1}
-         else{c(1, 2, 3, 4)[as.integer(group[, 2])[1]]}, 
+         else{rep(seq(1:6),ceiling(nlevels(group[, 2])/6))[as.integer(group[, 2])[1]]}, 
          col = col[as.integer(group[, 1])[1]])
     
     for (i in 2:ncol(counts)) 
     {
       lines(density(log2(counts[, i] + 1)), col = col[as.integer(group[,1])[i]], lwd = 2, 
             lty = if (ncol1) {1}
-            else {c(1, 2, 3, 4)[as.integer(group[, 2])[i]]})
+            else{rep(seq(1:6),ceiling(nlevels(group[, 2])/6))[as.integer(group[, 2])[i]]})
     }
     legend("topright", levels(group[, 1]), lty = 1, col = col[1:nlevels(group[,1])], lwd = 2, bty = "n")
-    if (!ncol1) legend("topleft", levels(group[, 2]), lty = c(1, 2, 3, 4)[1:nlevels(group[, 2])], col = 1, lwd = 2, bty = "n")
+    if (!ncol1) legend("topleft", levels(group[, 2]), lty = rep(seq(1:6),ceiling(nlevels(group[, 2])/6))[1:nlevels(group[, 2])], col = 1, lwd = 2, bty = "n")
     
   }
 

server.R

@@ -410,7 +410,7 @@ shinyServer(function(input, output,session) {
     if(!is.null(target)) 
     {
       namesTarget = colnames(target)[2:ncol(target)]
-      selectInput("InterestVar",h6(strong("Select the variables")),namesTarget,selected=namesTarget,multiple=TRUE)
+      selectInput("InterestVar",h6(strong("Select the variables")),namesTarget,selected=namesTarget[1],multiple=TRUE)
     }
   
   })
@@ -943,11 +943,13 @@ shinyServer(function(input, output,session) {
   
   output$VarIntDiag <- renderUI({
     
-    int = input$InterestVar
-    if(length(int)>=2) intSel = int[c(1,2)]
-    else intSel = int[1]
+    target=dataInputTarget()
     
-    selectizeInput("VarInt",h6(strong("Select the variables of interest (max 2)")),int, selected = intSel,multiple = TRUE,options = list(maxItems = 2))
+    if(!is.null(target)) 
+    {
+      namesTarget = colnames(target)[2:ncol(target)]
+      selectizeInput("VarInt",h6(strong("Select the variables of interest (max 2)")),namesTarget, selected = namesTarget[1],multiple = TRUE,options = list(maxItems = 2))
+    }
     
   })
   
@@ -1382,11 +1384,17 @@ output$RunButton <- renderUI({
   
   output$VarIntVisu <- renderUI({
     
-    int = input$InterestVar
-    if(length(int)>=2) intSel = int[c(1,2)]
-    else intSel = int[1]
-    
-    selectizeInput("VisuVarInt",h6(strong("Select the variables of interest")),int, selected = intSel,multiple = TRUE)
+#     int = input$InterestVar
+#     if(length(int)>=2) intSel = int[c(1,2)]
+#     else intSel = int[1]
+        
+      target=dataInputTarget()
+      
+      if(!is.null(target)) 
+      {
+        namesTarget = colnames(target)[2:ncol(target)]
+        selectizeInput("VisuVarInt",h6(strong("Select the variables of interest")),namesTarget, selected = namesTarget[1],multiple = TRUE)
+      }
     
   })
   #####################################################

ui.R

@@ -306,8 +306,7 @@ body <- dashboardBody(
                 box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
                   selectInput("DiagPlot","",c("Total barplot"="barplotTot","Nul barplot"="barplotNul",
                                               "Maj. taxonomy"="MajTax", "Density"="densityPlot", 
-                                              "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","Clustering" = "clustPlot",
-                                              "SERE" = "SERE"))
+                                              "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","Clustering" = "clustPlot"))
                     ),
                 box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,