From 5406c9c525478996f91e60fbb1fa5c0441b94173 Mon Sep 17 00:00:00 2001 From: Midoux Cedric <cedric.midoux@irstea.fr> Date: Tue, 19 Jun 2018 10:52:41 +0200 Subject: [PATCH] reorganisation des onglets --- server.R | 28 ++++++++++++++-------------- ui.R | 32 ++++++++++++++++---------------- 2 files changed, 30 insertions(+), 30 deletions(-) diff --git a/server.R b/server.R index 53e7d33..6bf0861 100644 --- a/server.R +++ b/server.R @@ -130,7 +130,7 @@ shinyServer validate( need( 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() @@ -188,7 +188,7 @@ shinyServer output$histo <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p <- plot_bar( physeq = data16S(), fill = input$barFill, @@ -251,7 +251,7 @@ shinyServer output$histoFocus <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p <- plot_composition( physeq = data16S(), taxaRank1 = input$focusRank, @@ -311,7 +311,7 @@ shinyServer output$clust <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) plot_clust( physeq = data16S(), dist = input$clustDist, @@ -380,7 +380,7 @@ shinyServer output$richnessA <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p <- plot_richness( physeq = data16S(), x = ifelse(is.null(checkNull( @@ -401,7 +401,7 @@ shinyServer output$richnessATable <- renderUI({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p(beautifulTable(data.frame( SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2) ))) @@ -422,7 +422,7 @@ shinyServer output$richnessB <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) beta <- melt(as(distance(data16S(), method = input$richnessBDist), "matrix")) colnames(beta) <- c("x", "y", "distance") @@ -493,7 +493,7 @@ shinyServer output$networkB <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) g <- make_network( data16S(), distance = input$richnessBDist, @@ -514,7 +514,7 @@ shinyServer output$richnessBTable <- renderUI({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p(beautifulTable(data.frame( SAMPLE = sample_names(data16S()), round(as.matrix( distance(data16S(), method = input$richnessBDist) @@ -524,7 +524,7 @@ shinyServer output$rarefactionCurve <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p <- ggrare( physeq = data16S(), step = 100, @@ -630,7 +630,7 @@ shinyServer output$Heatmap <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p <- plot_heatmap( physeq = prune_taxa(names(sort( taxa_sums(data16S()), decreasing = TRUE @@ -687,10 +687,10 @@ shinyServer output$tree <- renderPlot({ validate( - need(data16S(), "Need an abundance dataset"), + need(data16S(), "Requires an abundance dataset"), need( phy_tree(data16S(), errorIfNULL = FALSE), - "Need an phylogenetic tree" + "Requires a phylogenetic tree" ) ) p <- plot_tree( @@ -769,7 +769,7 @@ shinyServer output$acp <- renderPlot({ validate(need(data16S(), - "Need an abundance dataset")) + "Requires an abundance dataset")) p <- plot_samples( data16S(), ordination = ordinate( diff --git a/ui.R b/ui.R index b9938b9..b9aecbb 100644 --- a/ui.R +++ b/ui.R @@ -79,7 +79,7 @@ shinyUI(dashboardPage( uiOutput("histUI") ), tabPanel( - "Focus barplot", + "Filtered barplot", plotOutput("histoFocus", height = 700), box( title = "Paramètres", @@ -93,9 +93,14 @@ shinyUI(dashboardPage( ) ), tabPanel( - "Clustering", - plotOutput("clust", height = 700), - uiOutput("clustUI") + "Heatmap", + plotOutput("Heatmap", height = 700), + uiOutput("HeatmapUI") + ), + tabPanel( + "Rarefaction curves", + plotOutput("rarefactionCurve", height = 700), + uiOutput("rarefactionCurveUI") ), tabPanel(HTML("α-diversity"), box( @@ -138,9 +143,9 @@ shinyUI(dashboardPage( )) ), tabPanel( - "Rarefaction curves", - plotOutput("rarefactionCurve", height = 700), - uiOutput("rarefactionCurveUI") + "MultiDimensional Scaling", + plotOutput("acp", height = 700), + uiOutput("acpUI") ), tabPanel( "Phylogenetic tree", @@ -148,17 +153,12 @@ shinyUI(dashboardPage( uiOutput("treeUI") ), tabPanel( - "Heatmap", - plotOutput("Heatmap", height = 700), - uiOutput("HeatmapUI") - ), - tabPanel( - "MultiDimensional Scaling", - plotOutput("acp", height = 700), - uiOutput("acpUI") + "Clustering", + plotOutput("clust", height = 700), + uiOutput("clustUI") ), tabPanel( - "News features ...", + "Help", div( "Questions, problems or comments regarding this application should be sent to ", a(href = "mailto:cedric.midoux@irstea.fr?subject=[Easy16S]", "cedric.midoux@irstea.fr") -- GitLab