Commit 561ecddb authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Set tabbox size, shaman contact and update the tutorial

parent cf226001
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})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-72614324-2', 'auto');
ga('send', 'pageview');
if (!require("Rcpp")){
install.packages("Rcpp")
}
if(!require(shinydashboard)){
install.packages('shinydashboard')
library(shinydashboard)
}
if(!require(rjson)){
install.packages('rjson')
}
if(!require(devtools)){
install.packages('devtools')
}
#library(plotly)
if (!require(psych)) {
install.packages('psych')
library(psych)
}
if (!require(ggplot2)) {
install.packages('ggplot2')
library(ggplot2)
}
if (!require(vegan)) {
install.packages('vegan')
library(vegan)
}
if (!require(dendextend)) {
install.packages('dendextend')
library(dendextend)
}
if (!require(circlize)) {
install.packages('circlize')
library(circlize)
}
if (!require(d3heatmap)) {
install.packages('d3heatmap')
library(d3heatmap)
}
if (!require(biom)) {
install.packages('biom')
library(biom)
}
if (!require(devtools)) {
install.packages('devtools')
}
if (!require(rNVD3)) {
library(devtools)
install_github('rNVD3', 'ramnathv')
}
# Allow to upload 50M files
options(shiny.maxRequestSize=50*1024^2)
source("internal.R")
renderDataTable <- DT::renderDataTable
......@@ -246,13 +213,13 @@ shinyServer(function(input, output,session) {
data = tmp$data
check = tmp$check
cond = (!is.null(data$counts) && nrow(data$counts)>0)
res =infoBox(h6(strong("Counts table")), subtitle = h6("Load the counts table") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("upload"))
res =infoBox(h6(strong("Count table")), subtitle = h6("Load the count table") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("upload"))
if(cond)
{
if(!is.null(check$CheckCounts$Warning)) res = infoBox(h6(strong("Counts table")), subtitle = h6(check$CheckCounts$Warning), icon = icon("warning"),color = "orange",width=NULL,fill=TRUE)
if(!is.null(check$CheckCounts$Error)) res = infoBox(h6(strong("Counts table")), subtitle = h6(check$CheckCounts$Error), icon = icon("thumbs-o-down"),color = "red",width=NULL,fill=TRUE)
if(is.null(check$CheckCounts$Error) && is.null(check$CheckCounts$Warning)) res = infoBox(h6(strong("Counts table")), subtitle = h6(paste("Format of the counts table seems to be OK")), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
if(!is.null(check$CheckCounts$Warning)) res = infoBox(h6(strong("Count table")), subtitle = h6(check$CheckCounts$Warning), icon = icon("warning"),color = "orange",width=NULL,fill=TRUE)
if(!is.null(check$CheckCounts$Error)) res = infoBox(h6(strong("Count table")), subtitle = h6(check$CheckCounts$Error), icon = icon("thumbs-o-down"),color = "red",width=NULL,fill=TRUE)
if(is.null(check$CheckCounts$Error) && is.null(check$CheckCounts$Warning)) res = infoBox(h6(strong("Count table")), subtitle = h6(paste("Format of the count table seems to be OK")), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
}
return(res)
......@@ -367,8 +334,8 @@ 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 = "Counts table",
tabPanel("Counts table",dataTableOutput("DataCounts")),
tabBox(width = NULL, selected = "Count table",
tabPanel("Count table",dataTableOutput("DataCounts")),
tabPanel("Taxonomy",dataTableOutput("DataTaxo"))
)
}
......@@ -463,7 +430,7 @@ shinyServer(function(input, output,session) {
#### Ajout fontion check target
infoBox(h6(strong("Target file")), subtitle = h6("Your target file is OK"), icon = icon("thumbs-o-up"),color = "green",width=NULL,fill=TRUE)
}
else infoBox(h6(strong("Target file")), subtitle = h6("Label of the target file must correspond to counts table column names") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("warning"))
else infoBox(h6(strong("Target file")), subtitle = h6("Label of the target file must correspond to count table column names") ,color = "light-blue",width=NULL,fill=TRUE, icon = icon("warning"))
})
......@@ -492,7 +459,7 @@ shinyServer(function(input, output,session) {
if(!is.null(counts) && taxo != "...")
{
box(title=paste("Counts table (",taxo,")",sep=""),width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
box(title=paste("Count table (",taxo,")",sep=""),width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
dataTableOutput("CountsMerge"),
downloadButton('ExportCounts', 'Export normalised counts'),
downloadButton('ExportRelative', 'Export relative abundance')
......@@ -853,10 +820,8 @@ output$InfoContrast <- renderInfoBox({
## Run DESeq2 via RunDESeq button
observeEvent(input$RunDESeq,{
observeEvent(input$RunDESeq,{
withProgress(message="Analysis in progress...",ResDiffAnal())
})
......
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