Debug clustering and pca, plus some cometics

LoadPackages.R

@@ -66,11 +66,11 @@ if(!require(treeWeightD3)){
    devtools::install_github('pierreLec/treeWeightD3')
    library(treeWeightD3)
 }
-if (!require(BiocInstaller)){
-  source("https://bioconductor.org/biocLite.R")
-  biocLite("BiocInstaller")
-  library(BiocInstaller)
-}
+# if (!require(BiocInstaller)){
+#   source("https://bioconductor.org/biocLite.R")
+#   biocLite("BiocInstaller")
+#   library(BiocInstaller)
+# }
 
 if (!require(d3heatmap)) {
   devtools::install_github('aghozlane/d3heatmap')
@@ -263,3 +263,8 @@ if(!require("visNetwork")){
   install.packages("visNetwork")
   library(visNetwork)
 }
+
+if(!require("SummarizedExperiment")){
+  BiocManager::install("SummarizedExperiment")
+  library(SummarizedExperiment)
+}
\ No newline at end of file

Rfunctions/DiagPlot.R

@@ -138,7 +138,7 @@ HCPlot <- function (input,dds,group,type.trans=NULL,counts=NULL,CT,tree,col = c(
       ## Get the type of dendrogram
       type <- input$typeHculst
       
-      dend <- set(dend, "labels_cex", input$cexLabelDiag)
+      #dend <- set(dend, "labels_cex", input$cexLabelDiag)
       if(input$colorHC) labels_colors(dend)<-col[as.integer(as.factor(group))][order.dendrogram(dend)]
       if(type=="hori") 
       { 
@@ -148,7 +148,8 @@ HCPlot <- function (input,dds,group,type.trans=NULL,counts=NULL,CT,tree,col = c(
       else
       {
         par(cex=input$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$DistClust,"distance, Ward criterion",sep=" "))
+        res = circlize_dendrogram(dend, labels_track_height = 0.2, dend_track_height = .3, main = "Cluster dendrogram",xlab = paste(input$DistClust,"distance, Ward criterion",sep=" "), 
+                                  labels_cex = input$cexLabelDiag)
       }
     }
   }
@@ -554,8 +555,8 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
   { 
     type.trans <- type.trans[1]
     
-    if (type.trans == "VST") counts.trans <- assay(varianceStabilizingTransformation(dds))
-    else counts.trans <- assay(rlogTransformation(dds))
+    if (type.trans == "VST") counts.trans <- SummarizedExperiment::assay(varianceStabilizingTransformation(dds))
+    else counts.trans <- SummarizedExperiment::assay(rlogTransformation(dds))
     counts.trans = counts.trans[,ind_kept]
     
     rv = apply(counts.trans, 1, var, na.rm = TRUE)
@@ -754,8 +755,8 @@ Get_pca_table <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
   { 
     type.trans <- type.trans[1]
     
-    if (type.trans == "VST") counts.trans <- assay(varianceStabilizingTransformation(dds))
-    else counts.trans <- assay(rlogTransformation(dds))
+    if (type.trans == "VST") counts.trans <- SummarizedExperiment::assay(varianceStabilizingTransformation(dds))
+    else counts.trans <- SummarizedExperiment::assay(rlogTransformation(dds))
     counts.trans = counts.trans[,ind_kept]
     
     rv = apply(counts.trans, 1, var, na.rm = TRUE)

ui.R

@@ -1234,7 +1234,7 @@ function(request) {
                   ),
                   column(width=3,
                          box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
-                             selectizeInput("PlotVisuSelectComp","",c("Venn diagram"="Venn","Heatmap"="Heatmap_comp", "Logit plot"="LogitPlot", "p value density"="pValueDensity", "UpSet"="UpSet", "Multiple venn compair" = "multipleVenn"),selected = "Heatmap_comp")
+                             selectizeInput("PlotVisuSelectComp","",c("Venn diagram"="Venn", "UpSet"="UpSet", "Contrasts compair" = "multipleVenn" ,"Heatmap"="Heatmap_comp", "Logit plot"="LogitPlot", "Density plot"="pValueDensity"),selected = "Heatmap_comp")
                          ),
                          box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                              conditionalPanel(condition="input.PlotVisuSelectComp=='Heatmap_comp' || input.PlotVisuSelectComp=='UpSet' || input.PlotVisuSelectComp=='pValueDensity' || input.PlotVisuSelectComp=='multipleVenn'",