From 14bb24f6d052d44e4c94f25d8ed645e4ced61b79 Mon Sep 17 00:00:00 2001
From: Midoux Cedric <cedric.midoux@irstea.fr>
Date: Thu, 14 Jun 2018 14:51:23 +0200
Subject: [PATCH] SampleID
---
server.R | 20 ++--
ui.R | 315 +++++++++++++++++++++++++++----------------------------
2 files changed, 164 insertions(+), 171 deletions(-)
diff --git a/server.R b/server.R
index bcc438e..5fe94a7 100644
--- a/server.R
+++ b/server.R
@@ -27,7 +27,7 @@ shinyServer
options = list(
dom = "lBtip",
pageLength = 10,
- lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
+ lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')),
buttons = list(
'colvis',
list(
@@ -100,10 +100,11 @@ shinyServer
row.names = 1,
na.strings = NA
)
+ sample_data(d)$SampleID <- rownames(sample_data(d))
}
} else {
n <- data.frame(sample_names(d) , row.names = sample_names(d))
- names(n) <- "sample_names"
+ names(n) <- "SampleID"
sample_data(d) <- n
}
if (input$rareData) {
@@ -119,13 +120,9 @@ shinyServer
})
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)")
- }
+ validate(need(input$fileBiom, ""), need(input$demo == "input", ""))
+ paste("(min sample =", format(min(sample_sums(data16S(
+ ))), big.mark = " "), "reads)")
})
output$phyloseqPrint <- renderPrint({
@@ -743,10 +740,7 @@ shinyServer
selectInput(
"acpLabel",
label = "Label :",
- choices = c(
- "..." = 0,
- sample_variables(data16S())
- )
+ choices = c("..." = 0, sample_variables(data16S()))
),
selectInput(
"acpCol",
diff --git a/ui.R b/ui.R
index 75bb619..fa82fdf 100644
--- a/ui.R
+++ b/ui.R
@@ -7,174 +7,173 @@ shinyUI(dashboardPage(
selectInput(
"demo",
label = "Select demo data",
- choices = list(
- "Input data" = "input",
- "Chaillou et al., 2015" = "food"#,
- # "Mach et al., 2015" = "kinetic",
- # "Morton et al., 2017" = "soil",
- # "Ravel et al., 2011" = "ravel",
- #"GlobalPatterns" = "GlobalPatterns",
- #"biorare"
- ),
- selected = 1
- )
- ),
- hr(width = "90%"),
- tags$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"
+ choices = list("Input data" = "input",
+ "Chaillou et al., 2015" = "food"#,
+ # "Mach et al., 2015" = "kinetic",
+ # "Morton et al., 2017" = "soil",
+ # "Ravel et al., 2011" = "ravel",
+ #"GlobalPatterns" = "GlobalPatterns",
+ #"biorare"),
+ selected = 1
+ )
),
- 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")
+ hr(width = "90%"),
+ tags$div(
+ title = "Fichier d'abondance au format BIOM produit avec FROGS avec 'FROGS BIOM to std BIOM'",
+ fileInput(
+ "fileBiom",
+ label = h4("Fichier d'abondance :"),
+ placeholder = "data.biom"
+ ),
+ radioButtons(
+ "biomFormat",
+ label = NULL,
+ inline = TRUE,
+ choices = list(`STD BIOM` = "std",
+ `FROGS BIOM` = "frogs"),
+ selected = "std"
+ )
),
- tabPanel(
- "Histo global",
- plotOutput("histo", height = 700),
- uiOutput("histUI")
+ tags$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")
),
- tabPanel(
- "Histo selectif",
- plotOutput("histoFocus", height = 700),
- box(
- title = "Paramètres",
- width = NULL,
- status = "primary",
- uiOutput("histFocusUIfocusRank"),
- uiOutput("histFocusUIfocusTaxa"),
- uiOutput("histFocusUIfocusNbTaxa"),
- uiOutput("histFocusUIfocusGrid"),
- uiOutput("histFocusUIfocusX")
+ tags$div(
+ title = "Tableau de métadonnées avec en colonne les variables, en ligne les échantillons. \nAssurez vous de bien respecter l'ortographe des noms d'échantillons (1ère colonne). \nL'import d'une table excel est possible mais déconseillé.",
+ fileInput(
+ "fileMeta",
+ label = h4("Metadata :"),
+ placeholder = "data.csv"
)
),
- tabPanel(
- "Clustering",
- plotOutput("clust", height = 700),
- uiOutput("clustUI")
+ radioButtons(
+ "CSVsep",
+ label = "CSV Séparateur",
+ inline = TRUE,
+ choices = list(
+ `<tab>` = "\t",
+ `,` = ",",
+ `;` = ";",
+ excel = "excel"
+ )
),
- tabPanel("Richesse alpha", box(
- width = NULL, tabsetPanel(
- tabPanel(
- "Courbes",
- plotOutput("richnessA", height = 700),
- uiOutput("richnessAUI")
- ),
- tabPanel("Tables", uiOutput("richnessATable"))
+ tags$div(
+ title = "Arbre phylogéniques des OTU enracinné",
+ fileInput(
+ "fileTree",
+ label = h4("Arbre :"),
+ placeholder = "data.nwk"
)
- )),
- tabPanel(
- "Richesse beta",
- selectInput(
- "richnessBDist",
- label = "Distance :",
- choices = list(
- "bray",
- "jaccard",
- "unifrac",
- "wunifrac",
- "dpcoa",
- "jsd",
- "euclidean"
+ )#,
+ # 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")
)
),
- box(width = NULL, tabsetPanel(
- tabPanel(
- "Heatmap",
- plotOutput("richnessB", height = 700),
- uiOutput("richnessBUI")
- ),
- tabPanel(
- "Networks",
- plotOutput("networkB", height = 700),
- uiOutput("networkBUI")
+ tabPanel(
+ "Clustering",
+ plotOutput("clust", height = 700),
+ uiOutput("clustUI")
+ ),
+ tabPanel("Richesse alpha", box(
+ width = NULL, tabsetPanel(
+ tabPanel(
+ "Courbes",
+ 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"
+ )
),
- 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")
+ 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
--
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