diff --git a/panels/Summary-server.R b/panels/Summary-server.R
index bb9499c2c6c9574ffb0a133ae37758bd870c93f6..6b1e208b0241ceb1eb3b3c6764cba1a3dcc5ea0e 100644
--- a/panels/Summary-server.R
+++ b/panels/Summary-server.R
@@ -1,11 +1,11 @@
output$phyloseqPrint <- renderPrint({
validate(
need(
- data16S(),
+ physeq(),
"Firstly, you should select a demo dataset or upload an abundance BIOM file.\nFor example, with Galaxy, a BIOM file can be obtained at the end of FROGS workflow with the 'FROGS BIOM to std BIOM' tool. \nMake sure that the phyloseq object in the RData file is called 'data'."
)
)
- data16S()
+ physeq()
})
output$sampledataTable <- renderUI({
@@ -66,3 +66,5 @@ output$tableGlom <- DT::renderDataTable(server = FALSE, {
dplyr::select(-rowname)
beautifulTable(joinGlom)
})
+
+uiOutput("downloadUI")
diff --git a/panels/dataInput.R b/panels/dataInput.R
new file mode 100644
index 0000000000000000000000000000000000000000..d1ea368fee587316ea0ff937f423d62512194639
--- /dev/null
+++ b/panels/dataInput.R
@@ -0,0 +1,165 @@
+dataInput <- function(failed = FALSE) {
+ modalDialog(
+ title = "Select your data",
+
+ if (failed)
+ {
+ div(
+ "Invalide dataset. \n Please try again \n",
+ style = "font-weight: bold; color: red; text-align: center; white-space: pre-line"
+ )
+ },
+
+ "Firstly, you should select a demo dataset or upload an abundance BIOM file. For example, with Galaxy, a BIOM file can be obtained at the end of FROGS workflow with the `FROGS BIOM to std BIOM` tool. Make sure that the phyloseq object in the RData file is called `data`.",
+
+ radioButtons(
+ inputId = "dataset",
+ label = "Select dataset : ",
+ inline = TRUE,
+ choices = list(
+ "Demo" = "demo",
+ "Input data" = "input",
+ "Rdata" = "rdata"
+ ),
+ selected = "demo"
+ ),
+
+ wellPanel(uiOutput("dataUI")),
+
+ footer = tagList(modalButton("Cancel"),
+ actionButton(inputId = "okData", label = "OK"))
+ )
+}
+
+output$dataUI <- renderUI({
+ if (is.null(input$dataset))
+ return()
+
+ switch(
+ input$dataset,
+ "demo" = selectInput(
+ inputId = "demo",
+ label = "Select a demo dataset",
+ choices = c("Chaillou et al., 2015" = "food",
+ # "Mach et al., 2015" = "kinetic",
+ # "Morton et al., 2017" = "soil",
+ # "Ravel et al., 2011" = "ravel",
+ # "biorare" = "biorare",
+ "toto" = "toto",
+ "GlobalPatterns" = "GlobalPatterns")
+ ),
+ "input" = tags$div(
+ tags$div(
+ title = "Abundance BIOM file come from FROGS with 'FROGS BIOM to std BIOM', Qiime or another metagenomic tool.",
+ fileInput(
+ inputId = "fileBiom",
+ label = "Abundance BIOM file : ",
+ placeholder = "data.biom"
+ )
+ ),
+ radioButtons(
+ inputId = "biomFormat",
+ label = NULL,
+ inline = TRUE,
+ choices = c("STD BIOM" = "std",
+ "FROGS BIOM" = "frogs"),
+ selected = "std"
+ ),
+ # tags$div(
+ # style = "text-align:center",
+ # title = "Resample dataset such that all samples have the same library size. \nIt's using an random sampling without replacement.",
+ checkboxInput(
+ inputId = "rareData",
+ label = "Rarefy dataset",
+ value = TRUE
+ ),
+ # textOutput("rarefactionMin")
+ # ),
+ tags$div(
+ title = "Metadata table with variables (in columns) and samples (in rows). \nMake sure you follow the exact spelling of the sample names (1st column). \nThe import of an excel table is possible but not recommended.",
+ fileInput(
+ inputId = "fileMeta",
+ label = "Metadata table : ",
+ placeholder = "data.csv"
+ )
+ ),
+ radioButtons(
+ inputId = "CSVsep",
+ label = "CSV separator : ",
+ inline = TRUE,
+ choices = c("<tab>" = "\t",
+ "," = ",",
+ ";" = ";",
+ excel = "excel"
+ )
+ ),
+ fileInput(
+ inputId = "fileTree",
+ label = "Phylogenetic tree : ",
+ placeholder = "data.nwk"),
+ fileInput(
+ inputId = "fileSeq",
+ label = "Representative FASTA sequences of OTU : ",
+ placeholder = "data.fasta"
+ )
+ ),
+ "rdata" = fileInput(
+ inputId = "fileRData",
+ label = "RData where 'data' is a phyloseq object : ",
+ placeholder = "data.RData"
+ )
+ )
+})
+
+observeEvent(input$okData, {
+ physeq(NULL)
+ try(
+ physeq(
+ switch(
+ input$dataset,
+ "demo" =
+ {
+ data(GlobalPatterns)
+ load("demo/demo.RData")
+ get(input$demo)
+ },
+ "input" =
+ {
+ d <- .import_biom(input)
+ ## Format tax table
+ tax_table(d) <- .format_tax_table(tax_table(d))
+
+ ## import metadata and store it in phyloseq object
+ sample_data(d) <- .import_sample_data(input, d)
+
+ ## Rarefy data
+ if (input$rareData)
+ {
+ d <- rarefy_even_depth(
+ d,
+ replace = FALSE,
+ rngseed = as.integer(Sys.time()),
+ verbose = FALSE
+ )
+ }
+ d
+ },
+ "rdata" =
+ {
+ ne <- new.env()
+ if (!is.null(input$fileRData))
+ {load(input$fileRData$datapath, envir = ne)}
+ ne$data
+ }
+ )
+ ),
+ silent = TRUE,
+ outFile = showModal(dataInput(failed = TRUE))
+ )
+
+ if (class(physeq()) == "phyloseq") {
+ removeModal()
+ } else {
+ showModal(dataInput(failed = TRUE))
+ }
+})
diff --git a/server.R b/server.R
index b91ec4fbee2f853d45d819314886885fe4b704e0..1593d07301e8c56d4ea5d857d122de80f537a383 100644
--- a/server.R
+++ b/server.R
@@ -24,65 +24,13 @@ shinyServer
source("panels/pca-server.R", local = TRUE)
source("panels/tree-server.R", local = TRUE)
source("panels/cluster-server.R", local = TRUE)
-
- data16S <- reactive({
- ## BIOM input
- if (input$dataset == "input")
- {
- ## Unhappy path
- if (is.null(input$fileBiom))
- return()
-
- ## Happy path
- ## Import biom
- d <- .import_biom(input)
-
- ## Format tax table
- tax_table(d) <- .format_tax_table(tax_table(d))
-
- ## import metadata and store it in phyloseq object
- sample_data(d) <- .import_sample_data(input, d)
-
- ## Rarefy data
- if (input$rareData) {
- d <- rarefy_even_depth(
- d,
- replace = FALSE,
- rngseed = as.integer(Sys.time()),
- verbose = FALSE
- )
- }
- return(d)
- }
-
- ## Rdata input
- if (input$dataset == "rdata")
- {
- ## .import_from_rdata(input) ## does not work as a function for some reason
-
- ## Happy path
- ne <-
- new.env() ## new env to store RData content and avoid border effects
- if (!is.null(input$fileRData))
- load(input$fileRData$datapath, envir = ne)
- if (class(ne$data) == "phyloseq")
- return(ne$data)
-
- ## Unhappy paths: everything else
- return()
- }
-
- ## Default case
- load("demo/demo.RData")
- return(get(input$dataset))
-
+
+ physeq <- reactiveVal()
+
+ showModal(dataInput())
+
+ observeEvent(input$dataButton, {
+ showModal(dataInput())
})
- data <- reactiveValues()
- {
- observe({
- if (!is.null(data16S()))
- isolate(data <<- data16S())
- })
- }
})
diff --git a/ui.R b/ui.R
index 2b0db4512ec15c4a9f593ae699e677a10b6c56b4..af1890386d095f1a11952ad79307dfeae85b49f4 100644
--- a/ui.R
+++ b/ui.R
@@ -1,6 +1,6 @@
library(shinydashboard)
library(shinycustomloader)
-source("panels/Sidebar-ui.R", local = TRUE)
+#source("panels/Sidebar-ui.R", local = TRUE)
source("panels/Summary-ui.R", local = TRUE)
source("panels/barplot-ui.R", local = TRUE)
source("panels/heatmap-ui.R", local = TRUE)
@@ -18,7 +18,7 @@ dashboardHeader(title = "Easy16S"),
dashboardSidebar(
actionButton("dataButton", "Select your data"),
sidebarMenu(
- menuItem("Data", tabName = "Data", icon = icon("dashboard")),
+ #menuItem("Data", tabName = "Data", icon = icon("dashboard")),
menuItem("Summary", tabName = "Summary", icon = icon("dashboard")),
menuItem("Barplot", tabName = "barplot", icon = icon("dashboard")),
menuItem("Heatmap", tabName = "heatmap", icon = icon("dashboard")),
@@ -33,7 +33,7 @@ dashboardHeader(title = "Easy16S"),
)),
dashboardBody(
tabItems(
- tabItem(tabName = "Data", Sidebar),
+ #tabItem(tabName = "Data", Sidebar),
tabItem(tabName = "Summary", Summary),
tabItem(tabName = "barplot", barplot),
tabItem(tabName = "heatmap", heatmap),