Commit 5406c9c5 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

reorganisation des onglets

parent 83c268c8
...@@ -130,7 +130,7 @@ shinyServer ...@@ -130,7 +130,7 @@ shinyServer
validate( validate(
need( need(
data16S(), data16S(),
"Firsly, you should select a demo dataset or upload an abundance BIOM file.\nFor example, with Galaxy, this one can be obtained at the end of FROGS workflows with 'FROGS BIOM to std BIOM' tools" "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"
) )
) )
data16S() data16S()
...@@ -188,7 +188,7 @@ shinyServer ...@@ -188,7 +188,7 @@ shinyServer
output$histo <- renderPlot({ output$histo <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p <- plot_bar( p <- plot_bar(
physeq = data16S(), physeq = data16S(),
fill = input$barFill, fill = input$barFill,
...@@ -251,7 +251,7 @@ shinyServer ...@@ -251,7 +251,7 @@ shinyServer
output$histoFocus <- renderPlot({ output$histoFocus <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p <- plot_composition( p <- plot_composition(
physeq = data16S(), physeq = data16S(),
taxaRank1 = input$focusRank, taxaRank1 = input$focusRank,
...@@ -311,7 +311,7 @@ shinyServer ...@@ -311,7 +311,7 @@ shinyServer
output$clust <- renderPlot({ output$clust <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
plot_clust( plot_clust(
physeq = data16S(), physeq = data16S(),
dist = input$clustDist, dist = input$clustDist,
...@@ -380,7 +380,7 @@ shinyServer ...@@ -380,7 +380,7 @@ shinyServer
output$richnessA <- renderPlot({ output$richnessA <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p <- plot_richness( p <- plot_richness(
physeq = data16S(), physeq = data16S(),
x = ifelse(is.null(checkNull( x = ifelse(is.null(checkNull(
...@@ -401,7 +401,7 @@ shinyServer ...@@ -401,7 +401,7 @@ shinyServer
output$richnessATable <- renderUI({ output$richnessATable <- renderUI({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p(beautifulTable(data.frame( p(beautifulTable(data.frame(
SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2) SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2)
))) )))
...@@ -422,7 +422,7 @@ shinyServer ...@@ -422,7 +422,7 @@ shinyServer
output$richnessB <- renderPlot({ output$richnessB <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
beta <- beta <-
melt(as(distance(data16S(), method = input$richnessBDist), "matrix")) melt(as(distance(data16S(), method = input$richnessBDist), "matrix"))
colnames(beta) <- c("x", "y", "distance") colnames(beta) <- c("x", "y", "distance")
...@@ -493,7 +493,7 @@ shinyServer ...@@ -493,7 +493,7 @@ shinyServer
output$networkB <- renderPlot({ output$networkB <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
g <- make_network( g <- make_network(
data16S(), data16S(),
distance = input$richnessBDist, distance = input$richnessBDist,
...@@ -514,7 +514,7 @@ shinyServer ...@@ -514,7 +514,7 @@ shinyServer
output$richnessBTable <- renderUI({ output$richnessBTable <- renderUI({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p(beautifulTable(data.frame( p(beautifulTable(data.frame(
SAMPLE = sample_names(data16S()), round(as.matrix( SAMPLE = sample_names(data16S()), round(as.matrix(
distance(data16S(), method = input$richnessBDist) distance(data16S(), method = input$richnessBDist)
...@@ -524,7 +524,7 @@ shinyServer ...@@ -524,7 +524,7 @@ shinyServer
output$rarefactionCurve <- renderPlot({ output$rarefactionCurve <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p <- ggrare( p <- ggrare(
physeq = data16S(), physeq = data16S(),
step = 100, step = 100,
...@@ -630,7 +630,7 @@ shinyServer ...@@ -630,7 +630,7 @@ shinyServer
output$Heatmap <- renderPlot({ output$Heatmap <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p <- plot_heatmap( p <- plot_heatmap(
physeq = prune_taxa(names(sort( physeq = prune_taxa(names(sort(
taxa_sums(data16S()), decreasing = TRUE taxa_sums(data16S()), decreasing = TRUE
...@@ -687,10 +687,10 @@ shinyServer ...@@ -687,10 +687,10 @@ shinyServer
output$tree <- renderPlot({ output$tree <- renderPlot({
validate( validate(
need(data16S(), "Need an abundance dataset"), need(data16S(), "Requires an abundance dataset"),
need( need(
phy_tree(data16S(), errorIfNULL = FALSE), phy_tree(data16S(), errorIfNULL = FALSE),
"Need an phylogenetic tree" "Requires a phylogenetic tree"
) )
) )
p <- plot_tree( p <- plot_tree(
...@@ -769,7 +769,7 @@ shinyServer ...@@ -769,7 +769,7 @@ shinyServer
output$acp <- renderPlot({ output$acp <- renderPlot({
validate(need(data16S(), validate(need(data16S(),
"Need an abundance dataset")) "Requires an abundance dataset"))
p <- plot_samples( p <- plot_samples(
data16S(), data16S(),
ordination = ordinate( ordination = ordinate(
......
...@@ -79,7 +79,7 @@ shinyUI(dashboardPage( ...@@ -79,7 +79,7 @@ shinyUI(dashboardPage(
uiOutput("histUI") uiOutput("histUI")
), ),
tabPanel( tabPanel(
"Focus barplot", "Filtered barplot",
plotOutput("histoFocus", height = 700), plotOutput("histoFocus", height = 700),
box( box(
title = "Paramètres", title = "Paramètres",
...@@ -93,9 +93,14 @@ shinyUI(dashboardPage( ...@@ -93,9 +93,14 @@ shinyUI(dashboardPage(
) )
), ),
tabPanel( tabPanel(
"Clustering", "Heatmap",
plotOutput("clust", height = 700), plotOutput("Heatmap", height = 700),
uiOutput("clustUI") uiOutput("HeatmapUI")
),
tabPanel(
"Rarefaction curves",
plotOutput("rarefactionCurve", height = 700),
uiOutput("rarefactionCurveUI")
), ),
tabPanel(HTML("&alpha;-diversity"), tabPanel(HTML("&alpha;-diversity"),
box( box(
...@@ -138,9 +143,9 @@ shinyUI(dashboardPage( ...@@ -138,9 +143,9 @@ shinyUI(dashboardPage(
)) ))
), ),
tabPanel( tabPanel(
"Rarefaction curves", "MultiDimensional Scaling",
plotOutput("rarefactionCurve", height = 700), plotOutput("acp", height = 700),
uiOutput("rarefactionCurveUI") uiOutput("acpUI")
), ),
tabPanel( tabPanel(
"Phylogenetic tree", "Phylogenetic tree",
...@@ -148,17 +153,12 @@ shinyUI(dashboardPage( ...@@ -148,17 +153,12 @@ shinyUI(dashboardPage(
uiOutput("treeUI") uiOutput("treeUI")
), ),
tabPanel( tabPanel(
"Heatmap", "Clustering",
plotOutput("Heatmap", height = 700), plotOutput("clust", height = 700),
uiOutput("HeatmapUI") uiOutput("clustUI")
),
tabPanel(
"MultiDimensional Scaling",
plotOutput("acp", height = 700),
uiOutput("acpUI")
), ),
tabPanel( tabPanel(
"News features ...", "Help",
div( div(
"Questions, problems or comments regarding this application should be sent to ", "Questions, problems or comments regarding this application should be sent to ",
a(href = "mailto:cedric.midoux@irstea.fr?subject=[Easy16S]", "cedric.midoux@irstea.fr") a(href = "mailto:cedric.midoux@irstea.fr?subject=[Easy16S]", "cedric.midoux@irstea.fr")
......
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