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Commit 1a379492 authored by Amine GHOZLANE's avatar Amine GHOZLANE
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Remove useless save and clean DT call

parent 30e7ed5a
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.gitignore
View file @ 1a379492
......@@ -2,3 +2,4 @@
*.Rhistory
*.RData
.Rproj.user
*.Rproj
META16S_App.Rproj deleted 100644 → 0
View file @ 30e7ed5a
Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
Rfunctions/CompPlot.R
View file @ 1a379492
......@@ -252,6 +252,7 @@ GetData_venn <-function(input,SelContrast,BaseContrast,resDiff)
}
}
print(df.tot)
return(list(res=res,df.tot=df.tot))
}
Rfunctions/Data_Management.R
View file @ 1a379492
......@@ -195,7 +195,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
CT=CT_int
} else CT = CT[,ind]
save.image("test.RData")
#save.image("test.RData")
## Order CT according to the target
CT = OrderCounts(counts=CT,labels=labels)$CountsOrder
CT_noNorm = CT
......@@ -240,7 +240,7 @@ GetCountsMerge <- function(input,dataInput,taxoSelect,target,design)
## Keep normalized OTU table
CT_Norm = counts(dds, normalized=TRUE)
save(CT_Norm,dds,CT,taxo,taxoSelect,file="test.RData")
#save(CT_Norm,dds,CT,taxo,taxoSelect,file="test.RData")
# Only interesting OTU
# merged_table = merge(CT, taxo[order(rownames(CT)),], by="row.names")
merged_table = merge(CT, taxo, by="row.names")
......
Rfunctions/Stat_Model.R
View file @ 1a379492
......@@ -43,7 +43,7 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
}
countsNorm = counts(dds, normalized = TRUE)
save(dds,file="dds.RData")
#save(dds,file="dds.RData")
return(list(dds = dds,raw_counts=counts,countsNorm=countsNorm,target=target,design=design,normFactors = normFactorsOTU,CT_noNorm=CT_noNorm,CT_Norm=CT_Norm))
}
......
Rfunctions/VisuPlot.R
View file @ 1a379492
......@@ -413,6 +413,7 @@ Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE){
## Get interactivity
#ff = ggplotly(gg)
}
print(dataTmp)
return(list(plot=gg,dataDiv = dataTmp))
}
......
server.R
View file @ 1a379492
source('LoadPackages.R')
renderDataTable <- DT::renderDataTable
dataTableOutput <- DT::dataTableOutput
shinyServer(function(input, output,session) {
......@@ -308,25 +305,26 @@ shinyServer(function(input, output,session) {
#####################################################
## Counts Table
output$DataCounts <- renderDataTable(
output$DataCounts <- DT::renderDataTable(
dataInput()$data$counts,
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
## Counts Table
output$DataVenn<- renderDataTable({
SelContrast = input$ContrastList_table_FC
resDiff = ResDiffAnal()
BaseContrast = read.table(namesfile,header=TRUE)
GetData_venn(input,SelContrast,BaseContrast,resDiff)$df.tot
}, options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
output$DataVenn<- DT::renderDataTable(#{
#SelContrast = input$ContrastList_table_FC
#resDiff = ResDiffAnal()
#BaseContrast = read.table(namesfile,header=TRUE)
GetData_venn(input,input$ContrastList_table_FC,read.table(namesfile,header=TRUE),ResDiffAnal())$df.tot,
#}
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
## Taxonomy table
output$DataTaxo <- renderDataTable(
output$DataTaxo <- DT::renderDataTable(
dataInput()$data$taxo,
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
......@@ -341,8 +339,8 @@ shinyServer(function(input, output,session) {
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0)
{
tabBox(width = NULL, selected = "Count table",
tabPanel("Count table",dataTableOutput("DataCounts")),
tabPanel("Taxonomy",dataTableOutput("DataTaxo")),
tabPanel("Count table",DT::dataTableOutput("DataCounts")),
tabPanel("Taxonomy",DT::dataTableOutput("DataTaxo")),
tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"),
br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500))
)
......@@ -531,14 +529,14 @@ shinyServer(function(input, output,session) {
## target table
output$DataTarget <- renderDataTable(
output$DataTarget <- DT::renderDataTable(
dataInputTarget()$target,
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
## Counts table for the selected taxonomy level
output$CountsMerge <- renderDataTable(
output$CountsMerge <- DT::renderDataTable(
round(counts(ResDiffAnal()$dds,normalized=TRUE)),
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
......@@ -554,7 +552,7 @@ shinyServer(function(input, output,session) {
if(!is.null(counts) && taxo != "...")
{
box(title=paste("Count table (",taxo,")",sep=""),width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
dataTableOutput("CountsMerge"),
DT::dataTableOutput("CountsMerge"),
downloadButton('ExportCounts', 'Export normalised counts'),
downloadButton('ExportRelative', 'Export relative abundance')
)
......@@ -589,7 +587,7 @@ shinyServer(function(input, output,session) {
if(!is.null(target) && nrow(target)>0)
{
box(title="Target file overview",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
dataTableOutput("DataTarget")
DT::dataTableOutput("DataTarget")
)
}
......@@ -1145,7 +1143,7 @@ shinyServer(function(input, output,session) {
})
output$SizeFactTable <- renderDataTable(
output$SizeFactTable <- DT::renderDataTable(
SizeFactor_table(),
options = list(scrollX=TRUE,searching = FALSE, processing=FALSE
))
......@@ -1338,27 +1336,27 @@ shinyServer(function(input, output,session) {
})
## Significant diff table
output$DataDiffsignificant <- renderDataTable(
output$DataDiffsignificant <- DT::renderDataTable(
datatable(dataDiff()$significant,rownames = FALSE),
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
## Complete diff table
output$DataDiffcomplete <- renderDataTable(
output$DataDiffcomplete <- DT::renderDataTable(
datatable(dataDiff()$complete,rownames = FALSE),
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
## Up diff table
output$DataDiffup <- renderDataTable(
output$DataDiffup <- DT::renderDataTable(
datatable(dataDiff()$up,rownames = FALSE),
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
## Down diff table
output$DataDiffdown <- renderDataTable(
output$DataDiffdown <- DT::renderDataTable(
datatable(dataDiff()$down,rownames = FALSE),
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
......@@ -1374,10 +1372,10 @@ shinyServer(function(input, output,session) {
{
tabBox(width = NULL, selected = "Significant",
tabPanel("Significant",dataTableOutput("DataDiffsignificant")),
tabPanel("Complete",dataTableOutput("DataDiffcomplete")),
tabPanel("Up",dataTableOutput("DataDiffup")),
tabPanel("Down",dataTableOutput("DataDiffdown"))
tabPanel("Significant",DT::dataTableOutput("DataDiffsignificant")),
tabPanel("Complete",DT::dataTableOutput("DataDiffcomplete")),
tabPanel("Up",DT::dataTableOutput("DataDiffup")),
tabPanel("Down",DT::dataTableOutput("DataDiffdown"))
)
}
......@@ -1512,14 +1510,14 @@ shinyServer(function(input, output,session) {
## Regression coefficients Table
output$lmRegScatter <- renderDataTable(
output$lmRegScatter <- DT::renderDataTable(
Plot_Visu_Scatterplot(input,ResDiffAnal(),lmEst=TRUE)$regCoef,
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
## Correlation coefficients Table
output$CorTable <- renderDataTable(
output$CorTable <- DT::renderDataTable(
Plot_Visu_Scatterplot(input,ResDiffAnal(),CorEst=TRUE)$cor.est,
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
......@@ -1562,12 +1560,12 @@ shinyServer(function(input, output,session) {
})
output$Diversitytable <- renderDataTable({
output$Diversitytable <- DT::renderDataTable(
datatable({
resDiff = ResDiffAnal()
tmp = Plot_Visu_Diversity(input,resDiff)$dataDiv
tmp$VarX=NULL; tmp$VarCol=NULL
datatable(tmp[,c(4,5,1,2,3)],rownames= FALSE)
},
tmp[,c(4,5,1,2,3)]},rownames= FALSE),
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE, processing=FALSE
))
......
ui.R
View file @ 1a379492
......@@ -370,7 +370,7 @@ body <- dashboardBody(
br(),
conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
box(title = "Size factors", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
dataTableOutput("SizeFactTable"),
DT::dataTableOutput("SizeFactTable"),
fluidRow(
column(width=3,downloadButton('ExportSizeFactor', 'Export table')),
column(width=3,selectInput("sepsizef", h6(strong("Separator:")), c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";")))
......@@ -517,7 +517,7 @@ body <- dashboardBody(
column(width=6,
br(),
box(title = "Regression coefficients", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
dataTableOutput("lmRegScatter")
DT::dataTableOutput("lmRegScatter")
)
),
column(width=6,br(),htmlOutput("lmEquation"))
......@@ -528,7 +528,7 @@ body <- dashboardBody(
br(),
p(actionButton("scatterD3-reset-zoom", HTML("<span class='glyphicon glyphicon-search' aria-hidden='true'></span> Reset Zoom")),Align="right"),
box(title = "Correlation table", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
dataTableOutput("CorTable")
DT::dataTableOutput("CorTable")
)
),
......@@ -536,7 +536,7 @@ body <- dashboardBody(
conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
br(),
box(title = "Diversity values", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
dataTableOutput("Diversitytable"),
DT::dataTableOutput("Diversitytable"),
fluidRow(
column(width=3,downloadButton('ExportDiversitytable', 'Export table')),
column(width=3,selectInput("sepdiversity", "Separator:", c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";")))
......@@ -699,7 +699,7 @@ body <- dashboardBody(
column(width=9,
uiOutput("plotVisuComp"),
conditionalPanel(condition="input.PlotVisuSelectComp=='Venn'",
dataTableOutput("DataVenn")
DT::dataTableOutput("DataVenn")
)
),
column(width=3,
......
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