Commit e676c88e authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Be sure to use DESeq2shaman and improvement of treeweight

parent 73cdf25b
...@@ -35,7 +35,7 @@ GetInteraction2 <- function(target,VarInt) ...@@ -35,7 +35,7 @@ GetInteraction2 <- function(target,VarInt)
## Get the dds object of DESeq2 ## Get the dds object of DESeq2
Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,CT_Norm,tree=NULL) 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 sizeFactors(dds) = normFactorsOTU
ddstmp = NULL ddstmp = NULL
...@@ -63,18 +63,18 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C ...@@ -63,18 +63,18 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
# dds <- nbinomWaldTest(dds,modelMatrixType = "expanded") # dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
if(nrow(counts)*nrow(target)>=50000) 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$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE) # try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE)
# if(!is.null(ddstmp)) dds = ddstmp # if(!is.null(ddstmp)) dds = ddstmp
} }
if(nrow(counts)*nrow(target)<50000 || is.null(dds)) if(nrow(counts)*nrow(target)<50000 || is.null(dds))
{ {
dds <- estimateDispersions(dds, fitType=input$fitType) dds <- DESeq2shaman::estimateDispersions(dds, fitType=input$fitType)
dds <- nbinomWaldTest(dds) dds <- DESeq2shaman::nbinomWaldTest(dds)
} }
# dds <- DESeq(dds,fitType=input$fitType,modelMatrixType = "expanded",parallel = TRUE) # dds <- DESeq(dds,fitType=input$fitType,modelMatrixType = "expanded",parallel = TRUE)
# } # }
countsNorm = counts(dds, normalized = TRUE) countsNorm = DESeq2shaman::counts(dds, normalized = TRUE)
#save(dds,file="dds.RData") #save(dds,file="dds.RData")
......
...@@ -844,7 +844,7 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table) ...@@ -844,7 +844,7 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table)
nodeFind =input$selectTaxoPlot nodeFind =input$selectTaxoPlot
if(length(input$selectTaxoPlot) == 0) nodeFind = NULL if(length(input$selectTaxoPlot) == 0) nodeFind = NULL
#save(merge_dat,conditions,levels,nodeFind,file="abuntree.RDATA") #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) return(res)
......
...@@ -1174,7 +1174,15 @@ function(request) { ...@@ -1174,7 +1174,15 @@ function(request) {
column(width=6,sliderInput("lowerMargin", h6("Lower"),min=0,max=30,value = 6,step = 1)) 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 #### ### _______scatterplot ####
### ### ### ###
...@@ -1212,12 +1220,12 @@ function(request) { ...@@ -1212,12 +1220,12 @@ function(request) {
## ### ## ###
## _______common to several plots #### ## _______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) radioButtons(inputId = "SensPlotVisu",label = h6(strong("Orientation")),choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical",inline = TRUE)
) )
), ),
### _____Export #### ### _____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, box(title = "Export", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
conditionalPanel(condition="input.PlotVisuSelect=='Barplot'", conditionalPanel(condition="input.PlotVisuSelect=='Barplot'",
radioButtons("positionBarPlot","Position",c("Grouped"="dodge","Stacked"="fill"), selected = "fill",inline=TRUE) radioButtons("positionBarPlot","Position",c("Grouped"="dodge","Stacked"="fill"), selected = "fill",inline=TRUE)
......
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