From f61f2c175b9f913bbebba16a56fc981556649cc7 Mon Sep 17 00:00:00 2001
From: Midoux Cedric <cedric.midoux@irstea.fr>
Date: Tue, 27 Mar 2018 10:55:06 +0200
Subject: [PATCH] mise en ligne des scripts
---
server.R | 890 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
ui.R | 159 ++++++++++
2 files changed, 1049 insertions(+)
create mode 100644 server.R
create mode 100644 ui.R
diff --git a/server.R b/server.R
new file mode 100644
index 0000000..ef60663
--- /dev/null
+++ b/server.R
@@ -0,0 +1,890 @@
+library(shinydashboard)
+
+shinyServer
+(function(input, output, session)
+{
+ checkNull <- function(x) {
+ if (!exists(as.character(substitute(x)))) {
+ return(NULL)
+ } else if (is.null(x)) {
+ return(NULL)
+ } else if (length(x) > 1) {
+ return(x)
+ }
+ else if (x %in% c(0, "", NA, "NULL")) {
+ return(NULL)
+ } else {
+ return(x)
+ }
+ }
+
+ beautifulTable <- function(data) {
+ DT::datatable(
+ data = data,
+ rownames = FALSE,
+ filter = "top",
+ extensions = c("Buttons", "ColReorder", "FixedColumns"),
+ options = list(
+ dom = "lBtip",
+ pageLength = 10,
+ lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
+ buttons = list(
+ 'colvis',
+ list(
+ extend = 'collection',
+ buttons = c('copy', 'csv', 'excel', 'pdf'),
+ text = 'Download'
+ )
+ ),
+ colReorder = TRUE,
+ scrollX = TRUE,
+ fixedColumns = list(leftColumns = 1, rightColumns = 0)
+ ),
+ width = "auto",
+ height = "auto"
+ )
+ }
+
+ source(
+ "https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/R/load-extra-functions.R"
+ )
+
+ data16S <- reactive({
+ if (input$biomFormat == "std")
+ {
+ d <- import_biom(
+ BIOMfilename = input$fileBiom$datapath,
+ treefilename = input$fileTree$datapath,
+ refseqfilename = input$fileSeq$datapath
+ )
+ } else if (input$biomFormat == "frogs") {
+ d <- import_frogs(
+ biom = input$fileBiom$datapath,
+ treefilename = input$fileTree$datapath,
+ refseqfilename = input$fileSeq$datapath
+ )
+ }
+
+ colnames(tax_table(d)) <-
+ c("Kingdom",
+ "Phylum",
+ "Class",
+ "Order",
+ "Family",
+ "Genus",
+ "Species")
+ tax_table(d)[grep("unknown ", tax_table(d))] <- NA
+ #tax_table(d)[grep("Unclassified", tax_table(d))] <- NA
+ if (!is.null(input$fileMeta)) {
+ if (input$CSVsep == "excel") {
+ sample_data(d) <-
+ RcmdrMisc::readXL(input$fileMeta$datapath,
+ rownames = TRUE,
+ header = TRUE)
+ } else {
+ sample_data(d) <- read.csv(
+ input$fileMeta$datapath,
+ header = TRUE,
+ sep = input$CSVsep,
+ row.names = 1,
+ na.strings = NA
+ )
+ }
+ } else {
+ n <- data.frame(sample_names(d) , row.names = sample_names(d))
+ names(n) <- "sample_names"
+ sample_data(d) <- n
+ }
+ if (input$rareData) {
+ d <- rarefy_even_depth(
+ d,
+ replace = FALSE,
+ rngseed = as.integer(Sys.time()),
+ verbose = FALSE
+ )
+ }
+
+ return(d)
+ })
+
+ output$rarefactionMin <- renderText({
+ if (!is.null(input$fileBiom)) {
+ paste("(min sample =", format(min(sample_sums(data16S(
+
+ ))), big.mark = " "), "reads)")
+ } else {
+ paste("(min sample =", 0, "reads)")
+ }
+ })
+
+ output$rarefaction <- renderText({
+ if (input$rareData) {
+ "<font color=\"#FF0000\"><b> Vous travaillez acctuellement avec des données raréfiés </b></font>"
+ }
+ })
+
+ output$phyloseqPrint <- renderPrint({
+ validate(
+ need(
+ !is.null(input$fileBiom),
+ "Merci de commencer par importer un fichier d'abondance au format BIOM. Celui-ci peut etre obtenu a l'issue du workflow FROGS avec l'operation 'FROGS BIOM to std BIOM'"
+ )
+ )
+ data16S()
+ })
+
+ output$summaryTable <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ box(
+ title = "Tables",
+ width = NULL,
+ status = "primary",
+ tabsetPanel(
+ tabPanel("otu_table",
+ beautifulTable(
+ data.frame(OTU = taxa_names(data16S()), otu_table(data16S()))
+ )),
+ tabPanel("tax_table",
+ beautifulTable(
+ data.frame(OTU = taxa_names(data16S()), tax_table(data16S()))
+ )),
+ if (!is.null(input$fileMeta)) {
+ tabPanel("sample_data",
+ beautifulTable(data.frame(
+ SAMPLE = sample_names(data16S()), sample_data(data16S())
+ )))
+ }
+ )
+ )
+ })
+
+ output$histUI <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ selectInput(
+ "barFill",
+ label = "Niveau taxo :",
+ choices = rank_names(data16S())
+ ),
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "barGrid",
+ label = "Regroupement :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta))
+ {
+ selectInput("barX",
+ label = "X :",
+ choices = c("..." = 0, sample_variables(data16S())))
+ }
+ )
+ })
+
+ output$histo <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p <- plot_bar(
+ physeq = data16S(),
+ fill = input$barFill,
+ x = ifelse(is.null(checkNull(input$barX)), "Sample", input$barX)
+ )
+ if (!is.null(checkNull(input$barGrid))) {
+ p <-
+ p + facet_grid(paste(".", "~", input$barGrid), scales = "free_x")
+ }
+ return(p)
+ })
+
+ output$histFocusUIfocusRank <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ radioButtons(
+ "focusRank",
+ label = "Niveau taxo :",
+ choices = list(
+ "Kingdom" = 1,
+ "Phylum" = 2,
+ "Class" = 3,
+ "Order" = 4,
+ "Family" = 5,
+ "Genus" = 6
+ ),
+ inline = TRUE,
+ selected = 1
+ )
+ })
+
+ output$histFocusUIfocusTaxa <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ selectInput(
+ "focusTaxa",
+ label = "Taxa :",
+ choices = unique(as.matrix(as.data.frame(
+ tax_table(data16S())
+ )[, as.integer(input$focusRank)])),
+ selected = TRUE
+ )
+ })
+
+ output$histFocusUIfocusNbTaxa <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ sliderInput(
+ "focusNbTaxa",
+ label = "Nombre de sous-taxons :",
+ min = 0,
+ #max = sum(tax_table(tax_glom(data16S(), rank_names(data16S())[1+as.integer(input$focusRank)]))[, as.integer(input$focusRank)]==input$focusTaxa)
+ max = 30
+ ,
+ value = 10
+ )
+ })
+
+ output$histFocusUIfocusGrid <- renderUI({
+ if (is.null(input$fileBiom) && is.null(input$fileMeta))
+ return()
+ selectInput(
+ "focusGrid",
+ label = "Regroupement :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ })
+
+ output$histFocusUIfocusX <- renderUI({
+ if (is.null(input$fileBiom) && is.null(input$fileMeta))
+ return()
+ selectInput("focusX",
+ label = "X :",
+ choices = c("..." = 0, sample_variables(data16S())))
+ })
+
+ output$histoFocus <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p <- plot_composition(
+ physeq = data16S(),
+ taxaRank1 = rank_names(data16S())[as.integer(input$focusRank)],
+ taxaSet1 = input$focusTaxa,
+ taxaRank2 = rank_names(data16S())[as.integer(input$focusRank) + 1],
+ numberOfTaxa = input$focusNbTaxa,
+ fill = rank_names(data16S())[as.integer(input$focusRank) + 1],
+ x = ifelse(is.null(checkNull(input$focusX)), "Sample", input$focusX)
+ )
+ if (!is.null(checkNull(input$focusGrid))) {
+ p <-
+ p + facet_grid(paste(".", "~", input$focusGrid), scales = "free_x")
+ }
+
+ return(p)
+ })
+
+ output$clustUI <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ selectInput(
+ "clustDist",
+ label = "Distance :",
+ choices = list(
+ "bray",
+ "jaccard",
+ "unifrac",
+ "wunifrac",
+ "dpcoa",
+ "jsd",
+ "euclidean"
+ )
+ ),
+ selectInput(
+ "clustMethod",
+ label = "Methode :",
+ choices = list(
+ "ward.D2",
+ "ward.D",
+ "single",
+ "complete",
+ "average",
+ "mcquitty",
+ "median",
+ "centroid"
+ )
+ ),
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "clustCol",
+ label = "Couleur :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ }
+ )
+ })
+
+ output$clust <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ plot_clust(
+ physeq = data16S(),
+ dist = input$clustDist,
+ method = input$clustMethod,
+ color = checkNull(input$clustCol)
+ )
+ })
+
+ output$richnessAUI <- renderUI({
+ if (is.null(input$fileBiom)) {
+ return()
+ }
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ checkboxGroupInput(
+ "richnessMeasures",
+ label = "Mesures :",
+ choices = c(
+ "Observed",
+ "Chao1",
+ "ACE",
+ "Shannon",
+ "Simpson",
+ "InvSimpson",
+ "Fisher"
+ ),
+ selected = c(
+ "Observed",
+ "Chao1",
+ "ACE",
+ "Shannon",
+ "Simpson",
+ "InvSimpson",
+ "Fisher"
+ ),
+ inline = TRUE
+ ),
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "richnessX",
+ label = "X :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "richnessColor",
+ label = "Couleur :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "richnessShape",
+ label = "Forme :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ radioButtons(
+ "richnessBoxplot",
+ label = "Representation :",
+ choices = list(
+ "Points seuls" = 1,
+ "Boxplot et points" = 2,
+ "Boxplot seul" = 3
+ ),
+ selected = 2,
+ inline = TRUE
+ )
+ )
+ })
+
+ output$richnessA <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p <- plot_richness(
+ physeq = data16S(),
+ x = ifelse(is.null(checkNull(
+ input$richnessX
+ )), "samples", input$richnessX),
+ color = checkNull(input$richnessColor),
+ shape = checkNull(input$richnessShape),
+ measures = checkNull(input$richnessMeasures)
+ )
+ if (input$richnessBoxplot >= 2) {
+ p <- p + geom_boxplot()
+ }
+ if (input$richnessBoxplot <= 2) {
+ p <- p + geom_point()
+ }
+ return(p)
+ })
+
+ output$richnessATable <- renderUI({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p(beautifulTable(data.frame(
+ SAMPLE = sample_names(data16S()), round(estimate_richness(data16S()), digits = 2)
+ )))
+ })
+
+ output$richnessBUI <- renderUI({
+ if (is.null(input$fileMeta)) {
+ return()
+ }
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ selectInput(
+ "richnessOrder",
+ label = "Ordre de tri des echantillons :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ )
+ })
+
+ output$richnessB <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ beta <-
+ melt(as(distance(data16S(), method = input$richnessBDist), "matrix"))
+ colnames(beta) <- c("x", "y", "distance")
+ if (!is.null(checkNull(input$richnessOrder)))
+ {
+ new_factor = as.factor(get_variable(data16S(), input$richnessOrder))
+ variable_sort <-
+ as.factor(get_variable(data16S(), input$richnessOrder)[order(new_factor)])
+ L = levels(reorder(sample_names(data16S()), as.numeric(new_factor)))
+ beta$x <- factor(beta$x, levels = L)
+ beta$y <- factor(beta$y, levels = L)
+ palette <- hue_pal()(length(levels(new_factor)))
+ tipColor <-
+ col_factor(palette, levels = levels(new_factor))(variable_sort)
+ }
+ p <-
+ ggplot(beta, aes(x = x, y = y, fill = distance)) + geom_tile()
+ p <- p + theme(
+ axis.text.x = element_text(
+ angle = 90,
+ hjust = 1,
+ color = checkNull(tipColor)
+ ),
+ axis.text.y = element_text(color = checkNull(tipColor)),
+ axis.title.x = element_blank(),
+ axis.title.y = element_blank()
+ )
+ return(p + scale_fill_gradient2())
+ })
+
+ output$networkBUI <- renderUI({
+ if (is.null(input$fileBiom)) {
+ return()
+ }
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ sliderInput(
+ "netwMax",
+ label = "Cutoff :",
+ min = 0,
+ max = 1,
+ value = 0.7
+ ),
+ checkboxInput("netwOrphan",
+ label = "Garder les points orphelins",
+ value = TRUE),
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "netwCol",
+ label = "Couleur :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "netwShape",
+ label = "Forme :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "netwLabel",
+ label = "Label :",
+ choices = c(
+ select = "",
+ "Sample name" = "value",
+ sample_variables(data16S())
+ )
+ )
+ }
+ )
+ })
+
+ output$networkB <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ g <- make_network(
+ data16S(),
+ distance = input$richnessBDist,
+ max.dist = input$netwMax,
+ keep.isolates = input$netwOrphan
+ )
+ p <- plot_network(
+ g,
+ physeq = data16S(),
+ color = checkNull(input$netwCol),
+ shape = checkNull(input$netwShape),
+ label = checkNull(input$netwLabel),
+ hjust = 2,
+ title = NULL
+ )
+ return(p)
+ })
+
+ output$richnessBTable <- renderUI({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p(beautifulTable(data.frame(
+ SAMPLE = sample_names(data16S()), round(as.matrix(
+ distance(data16S(), method = input$richnessBDist)
+ ), digits = 2)
+ )))
+ })
+
+ output$rarefactionCurve <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p <- ggrare(
+ physeq = data16S(),
+ step = input$rarefactionStep,
+ color = checkNull(input$rarefactionColor),
+ se = FALSE
+ )
+ if (!is.null(checkNull(input$rarefactionGrid))) {
+ p <- p + facet_grid(paste(".", "~", input$rarefactionGrid))
+ }
+ if (!input$rareData)
+ {
+ if (input$rarefactionMin) {
+ p <-
+ p + geom_vline(xintercept = min(sample_sums(data16S())),
+ color = "gray60")
+ }
+ }
+
+ return(p)
+
+ })
+
+ output$rarefactionCurveUI <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ sliderInput(
+ "rarefactionStep",
+ label = "Etapes de calcul :",
+ min = 1,
+ max = 1000,
+ value = 100
+ ),
+ if (!input$rareData)
+ {
+ checkboxInput("rarefactionMin", label = "Afficher le seuil de l'echantillon minimal", value = TRUE)
+ },
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "rarefactionColor",
+ label = "Couleur :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "rarefactionGrid",
+ label = "Regroupement :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ }
+ )
+ })
+
+ output$HeatmapUI <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "heatmapGrid",
+ label = "Regroupement :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "heatmapX",
+ label = "X :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ sliderInput(
+ "heatmapTopOtu",
+ label = "Selection des n OTU les plus abondant :",
+ min = 1,
+ max = ntaxa(data16S()),
+ value = 250
+ ),
+ selectInput(
+ "heatmapDist",
+ label = "Distance :",
+ selected = "bray",
+ choices = list(
+ "bray",
+ "jaccard",
+ "unifrac",
+ "wunifrac",
+ "dpcoa",
+ "jsd",
+ "euclidean"
+ )
+ ),
+ selectInput(
+ "heatmapMethod",
+ label = "Methode :",
+ selected = "NMDS",
+ choices = list(
+ "NMDS",
+ "ward.D2",
+ "ward.D",
+ "single",
+ "complete",
+ "average",
+ "mcquitty",
+ "median",
+ "centroid"
+ )
+ )
+ )
+ })
+
+ output$Heatmap <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p <- plot_heatmap(
+ physeq = prune_taxa(names(sort(
+ taxa_sums(data16S()), decreasing = TRUE
+ )[1:input$heatmapTopOtu]), data16S()),
+ distance = input$heatmapDist,
+ method = input$heatmapMethod,
+ sample.order = checkNull(input$heatmapX),
+ low = "yellow",
+ high = "red",
+ na.value = "white"
+ )
+ if (!is.null(checkNull(input$heatmapGrid))) {
+ p <-
+ p + facet_grid(paste(".", "~", input$heatmapGrid), scales = "free_x")
+ }
+ return(p)
+ })
+
+ output$treeUI <- renderUI({
+ if (is.null(input$fileBiom) | is.null(input$fileTree))
+ return()
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ radioButtons(
+ "treeRank",
+ label = "Niveau taxonomique légendé :",
+ choices = list(
+ aucun = "",
+ "Kingdom",
+ "Phylum",
+ "Class",
+ "Order",
+ "Family",
+ "Genus",
+ "Species",
+ OTU = "taxa_names"
+ ),
+ inline = TRUE
+ ),
+ sliderInput(
+ "treeTopOtu",
+ label = "Selection des n OTU les plus abondant :",
+ min = 1,
+ max = ntaxa(data16S()),
+ value = 20
+ ),
+ checkboxInput("treeRadial", label = "Arbre radial", value = FALSE),
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "treeCol",
+ label = "Couleur :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta)) {
+ selectInput(
+ "treeShape",
+ label = "Forme :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ }
+ )
+ })
+
+ output$tree <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ validate(need(!is.null(input$fileTree),
+ "Merci d'importer un arbre"))
+ p <- plot_tree(
+ physeq = prune_taxa(names(sort(
+ taxa_sums(data16S()), decreasing = TRUE
+ )[1:input$treeTopOtu]), data16S()),
+ color = checkNull(input$treeCol),
+ shape = checkNull(input$treeShape),
+ size = "abundance",
+ label.tips = checkNull(input$treeRank),
+ sizebase = 2,
+ ladderize = "left",
+ plot.margin = 0
+ )
+ if (checkNull(input$treeRadial)) {
+ return(p + coord_polar(theta = "y"))
+ } else {
+ return(p)
+ }
+ })
+
+ output$acpUI <- renderUI({
+ if (is.null(input$fileBiom))
+ return()
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ selectInput(
+ "acpDist",
+ label = "Distance :",
+ selected = "bray",
+ choices = list(
+ "bray",
+ "jaccard",
+ "unifrac",
+ "wunifrac",
+ "dpcoa",
+ "jsd",
+ "euclidean"
+ )
+ ),
+ selectInput(
+ "acpMethod",
+ label = "Methode :",
+ selected = "MDS",
+ choices = list("DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA")
+ ),
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "acpCol",
+ label = "Couleur :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "acpShape",
+ label = "Forme :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "acpEllipse",
+ label = "Ellipses :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ },
+ if (!is.null(input$fileMeta))
+ {
+ selectInput(
+ "acpRep",
+ label = "Barycentre :",
+ choices = c("..." = 0, sample_variables(data16S()))
+ )
+ }
+ )
+ })
+
+ output$acp <- renderPlot({
+ validate(need(
+ !is.null(input$fileBiom),
+ "Merci d'importer un fichier d'abondance"
+ ))
+ p <- plot_samples(
+ data16S(),
+ ordination = ordinate(
+ data16S(),
+ method = input$acpMethod,
+ distance = input$acpDist
+ ),
+ axes = c(1, 2),
+ color = checkNull(input$acpCol),
+ replicate = checkNull(input$acpRep),
+ shape = checkNull(input$acpShape)
+ )
+ if (!is.null(checkNull(input$acpEllipse))) {
+ p <- p + stat_ellipse(aes_string(group = input$acpEllipse))
+ }
+ return(p + theme_bw())
+ })
+})
\ No newline at end of file
diff --git a/ui.R b/ui.R
new file mode 100644
index 0000000..5154a3b
--- /dev/null
+++ b/ui.R
@@ -0,0 +1,159 @@
+library(shinydashboard)
+shinyUI(dashboardPage(
+ dashboardHeader(title = "Easy16S"),
+ dashboardSidebar(
+ tags$div(
+ title = "Fichier d'abondance au format BIOM produit avec FROGS avec 'FROGS BIOM to std BIOM'",
+ fileInput(
+ "fileBiom",
+ label = h4("Fichier d'abondance :"),
+ placeholder = "data.biom"
+ ),
+ radioButtons(
+ "biomFormat",
+ label = NULL,
+ inline = TRUE,
+ choices = list(`STD BIOM` = "std",
+ `FROGS BIOM` = "frogs"),
+ selected = "std"
+ )
+ ),
+ tags$div(
+ style = "text-align:center",
+ title = "Rarefier les données avec un tirage aléatoire pour supprimer l'effet de la profondeur de séquençage",
+ checkboxInput("rareData", label = "Rarefier les donnees.", value = TRUE),
+ textOutput("rarefactionMin")
+ ),
+ tags$div(
+ title = "Tableau de métadonnées avec en colonne les variables, en ligne les échantillons. \nAssurez vous de bien respecter l'ortographe des noms d'échantillons (1ère colonne). \nL'import d'une table excel est possible mais déconseillé.",
+ fileInput(
+ "fileMeta",
+ label = h4("Metadata :"),
+ placeholder = "data.csv"
+ )
+ ),
+ radioButtons(
+ "CSVsep",
+ label = "CSV Séparateur",
+ inline = TRUE,
+ choices = list(
+ `<tab>` = "\t",
+ `,` = ",",
+ `;` = ";",
+ excel = "excel"
+ )
+ ),
+ tags$div(
+ title = "Arbre phylogéniques des OTU enracinné",
+ fileInput(
+ "fileTree",
+ label = h4("Arbre :"),
+ placeholder = "data.nwk"
+ )
+ ),
+ tags$div(
+ title = "Séquences FASTA des OTU",
+ fileInput(
+ "fileSeq",
+ label = h4("Séquences de references :"),
+ placeholder = "data.fasta"
+ )
+ )
+ ),
+ dashboardBody(
+ tabsetPanel(
+ tabPanel(
+ "Summary",
+ verbatimTextOutput("phyloseqPrint"),
+ uiOutput("summaryTable")
+ ),
+ tabPanel(
+ "Histo global",
+ plotOutput("histo", height = 700),
+ uiOutput("histUI")
+ ),
+ tabPanel(
+ "Histo selectif",
+ plotOutput("histoFocus", height = 700),
+ box(
+ title = "Paramètres",
+ width = NULL,
+ status = "primary",
+ uiOutput("histFocusUIfocusRank"),
+ uiOutput("histFocusUIfocusTaxa"),
+ uiOutput("histFocusUIfocusNbTaxa"),
+ uiOutput("histFocusUIfocusGrid"),
+ uiOutput("histFocusUIfocusX")
+ )
+ ),
+ tabPanel(
+ "Clustering",
+ plotOutput("clust", height = 700),
+ uiOutput("clustUI")
+ ),
+ tabPanel("Richesse alpha", box(
+ width = NULL, tabsetPanel(
+ tabPanel(
+ "Courbes",
+ htmlOutput("rarefaction"),
+ plotOutput("richnessA", height = 700),
+ uiOutput("richnessAUI")
+ ),
+ tabPanel("Tables", uiOutput("richnessATable"))
+ )
+ )),
+ tabPanel(
+ "Richesse beta",
+ selectInput(
+ "richnessBDist",
+ label = "Distance :",
+ choices = list(
+ "bray",
+ "jaccard",
+ "unifrac",
+ "wunifrac",
+ "dpcoa",
+ "jsd",
+ "euclidean"
+ )
+ ),
+ box(width = NULL, tabsetPanel(
+ tabPanel(
+ "Heatmap",
+ plotOutput("richnessB", height = 700),
+ uiOutput("richnessBUI")
+ ),
+ tabPanel(
+ "Networks",
+ plotOutput("networkB", height = 700),
+ uiOutput("networkBUI")
+ ),
+ tabPanel("Tables", uiOutput("richnessBTable"))
+ ))
+ ),
+ tabPanel(
+ "Courbe de rarefaction",
+ plotOutput("rarefactionCurve", height = 700),
+ uiOutput("rarefactionCurveUI")
+ ),
+ tabPanel(
+ "Arbre phylo",
+ plotOutput("tree", height = 700),
+ uiOutput("treeUI")
+ ),
+ tabPanel(
+ "Heatmap",
+ plotOutput("Heatmap", height = 700),
+ uiOutput("HeatmapUI")
+ ),
+ tabPanel("Analyses multivariées", plotOutput("acp", height = 700), uiOutput("acpUI")),
+ tabPanel(
+ "et plus ...",
+ div(
+ "Merci d'adresser vos remarques, bugs, demandes, besoins et conseils à ",
+ a(href = "mailto:cedric.midoux@irstea.fr?subject=[Easy16S]", "cedric.midoux@irstea.fr")
+ )
+ )
+ )
+ )
+))
\ No newline at end of file
--
GitLab