Commit 2ff96c4c authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Few debug and add separator

parent 3538d310
*.Rproj.user
*.Rhistory
*.RData
.Rproj.user
......@@ -29,7 +29,7 @@ shinyServer(function(input, output,session) {
if (is.null(inFile)) return(NULL)
data = read.csv(inFile$datapath,sep="\t",header=TRUE,check.names=FALSE)
data = read.csv(inFile$datapath,sep=input$sepcount,header=TRUE,check.names=FALSE)
colnames(data) = gsub("-",".",colnames(data))
## Rownames
......@@ -49,7 +49,7 @@ shinyServer(function(input, output,session) {
if(input$TypeTaxo=="Table")
{
data = read.csv(inFile$datapath,sep="\t",header=TRUE)
data = read.csv(inFile$datapath,sep=input$septaxo,header=TRUE)
## Rownames
if(!TRUE%in%duplicated(data[,1])){
......@@ -134,7 +134,7 @@ shinyServer(function(input, output,session) {
if (is.null(inFile)) return(NULL)
data = read.csv(inFile$datapath,sep="\t",header=TRUE)
data = read.csv(inFile$datapath,sep=input$sepsize,header=TRUE)
return(as.data.frame(data))
})
......
......@@ -147,8 +147,13 @@ body <- dashboardBody(
"- PCA",br(),img(src="tutorial/tutorial_pca.png",width = "100%",style="max-width: 900px"),hr(),
"- PCOA",br(),img(src="tutorial/tutorial_pcoa.png",width = "100%",style="max-width: 900px"),hr(),
"- Clustering",br(),img(src="tutorial/tutorial_clustering.png",width = "100%",style="max-width: 900px"))),
tabPanel("4-Differential analysis results",
img(src = "tutorial/tutorial_table.png",width = "100%",style="max-width: 900px")),
tabPanel("4-Tables",
p("'Tables' section provides the results of the differential analysis.
For one given contrast, we have:",br(),
"- The id of the given taxonomical level",br(),
"- The base mean is the mean normalized count for the given annotation of all samples.",br(),
"- The fold change .",br(),
img(src = "tutorial/tutorial_table.png",width = "100%",style="max-width: 900px"))),
tabPanel("5-Visualization",
p("'Diagnostic plots' section provides several visualization to control the analysis",br(),
"- Barplot",br(),img(src="tutorial/tutorial_barplot.png",width = "100%",style="max-width: 900px"),hr(),
......@@ -229,19 +234,27 @@ body <- dashboardBody(
selectInput("FileFormat","",c("Count table & taxonomy"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts")
),
conditionalPanel(condition="input.FileFormat=='fileCounts'",
box(title="Load the count table",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
box(title="Load the count table",width = 3,height = "260px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
fluidRow(
column(width=6,radioButtons("TypeTable",h6(strong("Type:")),c("OTU/Gene table"="OTU","MGS table"="MGS")))
column(width=6,radioButtons("TypeTable",h6(strong("Type:")),c("OTU/Gene table"="OTU","MGS table"="MGS"))),
column(width=6,selectInput("sepcount", h6(strong("Separator:")),
c("\\t" = "\t",
"," = ",",
";" = ";")))
),
fileInput('fileCounts', h6(strong('Select your file')),width="100%")
),
box(title="Load the taxonomy file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
box(title="Load the taxonomy file",width = 3,height = "260px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
fluidRow(
column(width=6,radioButtons("TypeTaxo",h6(strong("Format:")),c("Table"="Table","RDP"="RDP"))),
column(width=6,
conditionalPanel(condition="input.TypeTaxo=='RDP'",numericInput("RDP_th",h6(strong("Threshold:")),0.5,step=0.01,min=0.01,max=1))
)
),
column(width=6,
conditionalPanel(condition="input.TypeTaxo=='Table'",selectInput("septaxo", h6(strong("Separator:")),
c("\\t" = "\t", "," = ",", ";" = ";")))
)
),
fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
)
......@@ -249,7 +262,7 @@ body <- dashboardBody(
),
conditionalPanel(condition="input.FileFormat=='fileBiom'",
box(title="Load the BIOM file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
box(title="Load the BIOM file",width = 3, status = "primary", solidHeader = TRUE,collapsible = FALSE,
fileInput('fileBiom', h5(strong('Select your file')),width="100%")
)
)
......@@ -274,8 +287,9 @@ body <- dashboardBody(
column(width=5,
box(title="Experimental design",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
fluidRow(
column(width=6,fileInput('fileTarget', h6(strong('Select your target file')),width="100%")),
column(width=6,uiOutput("SelectTaxo"))
column(width=5,fileInput('fileTarget', h6(strong('Select your target file')),width="100%")),
column(width=2,selectInput("septarget", h6(strong("Separator:")), c("\\t" = "\t", "," = ",", ";" = ";"))),
column(width=5,uiOutput("SelectTaxo"))
),
fluidRow(
column(width=6,uiOutput("SelectInterestVar")),
......@@ -327,6 +341,7 @@ body <- dashboardBody(
column(width=3,
fileInput('fileSizeFactors', h6(strong('Define your own size factors')),width="100%")
),
column(width=3, selectInput("sepsize", h6(strong("Separator:")), c("\\t" = "\t", "," = ",", ";" = ";"))),
column(width=3,br(),htmlOutput("InfoSizeFactor"))
)
),
......
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