Be sure to use DESeq2shaman and improvement of treeweight

Rfunctions/Stat_Model.R

@@ -35,7 +35,7 @@ GetInteraction2 <- function(target,VarInt)
 ## Get the dds object of DESeq2
 Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,CT_Norm,tree=NULL)
 {
-  dds <- DESeqDataSetFromMatrix(countData=counts, colData=target, design=design,ignoreRank = TRUE)
+  dds <- DESeq2shaman::DESeqDataSetFromMatrix(countData=counts, colData=target, design=design,ignoreRank = TRUE)
   sizeFactors(dds) = normFactorsOTU
   ddstmp = NULL
   
@@ -63,18 +63,18 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
     # dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
    if(nrow(counts)*nrow(target)>=50000)
     {
-     dds = DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf)
+     dds = DESeq2shaman::DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf)
         # try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE)
         # if(!is.null(ddstmp)) dds = ddstmp
     }
    if(nrow(counts)*nrow(target)<50000 || is.null(dds))
     {
-        dds <- estimateDispersions(dds, fitType=input$fitType)
-        dds <- nbinomWaldTest(dds)
+        dds <- DESeq2shaman::estimateDispersions(dds, fitType=input$fitType)
+        dds <- DESeq2shaman::nbinomWaldTest(dds)
     }
     # dds <-  DESeq(dds,fitType=input$fitType,modelMatrixType = "expanded",parallel = TRUE)
   # }
-  countsNorm = counts(dds, normalized = TRUE)
+  countsNorm = DESeq2shaman::counts(dds, normalized = TRUE)
   
   
   #save(dds,file="dds.RData")

Rfunctions/VisuPlot.R

@@ -844,7 +844,7 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table)
       nodeFind =input$selectTaxoPlot
       if(length(input$selectTaxoPlot) == 0) nodeFind = NULL
       #save(merge_dat,conditions,levels,nodeFind,file="abuntree.RDATA")
-      res = treeWeightD3(merge_dat,conditions,levels,nodeFind=nodeFind, height =input$heightVisu+10, width=if(input$modifwidthVisu){input$widthVisu})
+      res = treeWeightD3(merge_dat,conditions,levels,nodeFind=nodeFind, height =input$heightVisu+10, width=if(input$modifwidthVisu){input$widthVisu}, input$isColorRandom, input$colorLevel)
     }
   }
   return(res)

ui.R

@@ -1174,7 +1174,15 @@ function(request) {
                                                 column(width=6,sliderInput("lowerMargin", h6("Lower"),min=0,max=30,value = 6,step = 1))
                                               )
                              ),
-                             
+                             ###            ###
+                             ### _______TreeWeightplot ####
+                             ###            ###
+                             conditionalPanel(condition="input.PlotVisuSelect=='Tree'",
+                                              fluidRow(
+                                                column(width=12,checkboxInput("isColorRandom", "Random colors", value = FALSE)),
+                                                column(width=12,sliderInput("colorLevel", h6("Color Level"),min=1,max=4,value = 1,step = 1))
+                                              )
+                             ),
                              ###            ###
                              ### _______scatterplot ####
                              ###            ###
@@ -1212,12 +1220,12 @@ function(request) {
                              ##           ###
                              ## _______common to several plots ####
                              ###          ###
-                             conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Scatterplot' && input.PlotVisuSelect!='Krona' && input.PlotVisuSelect!='Phylogeny' && input.PlotVisuSelect!='Network'",
+                             conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Scatterplot' && input.PlotVisuSelect!='Krona' && input.PlotVisuSelect!='Tree' && input.PlotVisuSelect!='Phylogeny' && input.PlotVisuSelect!='Network'",
                                               radioButtons(inputId = "SensPlotVisu",label = h6(strong("Orientation")),choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical",inline = TRUE)
                              )
                          ),
                          ### _____Export ####
-                         conditionalPanel(condition="input.PlotVisuSelect!='Krona' && input.PlotVisuSelect!='Phylogeny' ",
+                         conditionalPanel(condition="input.PlotVisuSelect!='Krona' && input.PlotVisuSelect!='Phylogeny' && input.PlotVisuSelect!='Tree'",
                                           box(title = "Export",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                                               conditionalPanel(condition="input.PlotVisuSelect=='Barplot'",
                                                                radioButtons("positionBarPlot","Position",c("Grouped"="dodge","Stacked"="fill"), selected = "fill",inline=TRUE)