Commit 3fedc910 authored by svolant's avatar svolant
Browse files

Loading bar

parent a67b11b4
......@@ -3,6 +3,7 @@ library(shiny)
renderDataTable <- DT::renderDataTable
dataTableOutput <- DT::dataTableOutput
shinyServer(function(input, output,session) {
hide(id = "loading-content", anim = TRUE, animType = "fade",time=1.5)
......@@ -185,7 +186,7 @@ shinyServer(function(input, output,session) {
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(taxo) && taxo!="..." && !is.null(target))
{
design = GetDesign(input)
tmp = isolate(GetCountsMerge(input,data,taxo,target,design))
tmp = isolate(withProgress(GetCountsMerge(input,data,taxo,target,design),message="Merging the counts ..."))
counts = tmp$counts
CheckTarget = tmp$CheckTarget
#target = tmp$target
......@@ -294,13 +295,9 @@ shinyServer(function(input, output,session) {
menuSubItem("Comparison plots",tabName="CompPlot"),
tabName = "Visu"),
menuItem("Perspective plots", icon = icon("pie-chart"), tabName = "Krona")
)
}
else{
sidebarMenu()
}
})
......@@ -333,7 +330,7 @@ shinyServer(function(input, output,session) {
output$DataTaxo <- renderDataTable(
dataInput()$data$taxo,
options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
pageLength = 10,scrollX=TRUE
pageLength = 10,scrollX=TRUE, processing=FALSE
))
......@@ -993,29 +990,28 @@ shinyServer(function(input, output,session) {
## Get the results from DESeq2
ResDiffAnal <-eventReactive(input$RunDESeq,{
ResDiffAnal <-eventReactive(input$RunDESeq,withProgress({
target = dataInputTarget()$target
design = GetDesign(input)
counts = dataMergeCounts()$counts
CT_noNorm = dataMergeCounts()$CT_noNorm
CT_Norm = dataMergeCounts()$CT_Norm
dMC = dataMergeCounts()
counts = dMC$counts
CT_noNorm = dMC$CT_noNorm
CT_Norm = dMC$CT_Norm
## If no file, size factors are estimated
normFactors = SizeFactors_fromFile()$normFactors
Get_dds_object(input,counts,target,design,normFactors,CT_noNorm,CT_Norm)
})
},message = "Analysis in progress"))
## Run DESeq2 via RunDESeq button
observeEvent(input$RunDESeq,{
withProgress(message="Analysis in progress...",ResDiffAnal())
ResDiffAnal()
})
#####################################################
##
......
......@@ -5,7 +5,7 @@ library(shinythemes)
library(shinyjs)
function(request) {
sidebar <- dashboardSidebar(
useShinyjs(),
inlineCSS(appCSS),
......@@ -20,6 +20,7 @@ sidebar <- dashboardSidebar(
menuItem("Home", tabName = "Home", icon = icon("home")),
menuItem("Tutorial", tabName = "Tutorial", icon = icon("book")),
menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
# bookmarkButton(),
menuItemOutput("dymMenu"),
img(src = "logo.jpg", height = 49, width = 220,style="position:absolute;bottom:0;margin:0 0 15px 10px;")
)
......@@ -714,11 +715,13 @@ body <- dashboardBody(
dbHeader$children[[2]]$children <- tags$a(tags$img(src='akuaku.png',height='40',width='50',style="margin:5px 0 5px 0;",align='left'), tags$h3("SHAMAN",style="font-family:Purisa; margin:15px 25px 5px 0;color:white;"))
# Put them together into a dashboardPage
dashboardPage(skin="blue",
dashboardPage(skin="blue",
dbHeader,
sidebar,
body
)
}
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