Commit 14bb24f6 authored by Midoux Cedric's avatar Midoux Cedric
Browse files

SampleID

parent 1a144e0a
...@@ -27,7 +27,7 @@ shinyServer ...@@ -27,7 +27,7 @@ shinyServer
options = list( options = list(
dom = "lBtip", dom = "lBtip",
pageLength = 10, 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( buttons = list(
'colvis', 'colvis',
list( list(
...@@ -100,10 +100,11 @@ shinyServer ...@@ -100,10 +100,11 @@ shinyServer
row.names = 1, row.names = 1,
na.strings = NA na.strings = NA
) )
sample_data(d)$SampleID <- rownames(sample_data(d))
} }
} else { } else {
n <- data.frame(sample_names(d) , row.names = sample_names(d)) n <- data.frame(sample_names(d) , row.names = sample_names(d))
names(n) <- "sample_names" names(n) <- "SampleID"
sample_data(d) <- n sample_data(d) <- n
} }
if (input$rareData) { if (input$rareData) {
...@@ -119,13 +120,9 @@ shinyServer ...@@ -119,13 +120,9 @@ shinyServer
}) })
output$rarefactionMin <- renderText({ output$rarefactionMin <- renderText({
if (!is.null(input$fileBiom)) { validate(need(input$fileBiom, ""), need(input$demo == "input", ""))
paste("(min sample =", format(min(sample_sums(data16S( paste("(min sample =", format(min(sample_sums(data16S(
))), big.mark = " "), "reads)")
))), big.mark = " "), "reads)")
} else {
paste("(min sample =", 0, "reads)")
}
}) })
output$phyloseqPrint <- renderPrint({ output$phyloseqPrint <- renderPrint({
...@@ -743,10 +740,7 @@ shinyServer ...@@ -743,10 +740,7 @@ shinyServer
selectInput( selectInput(
"acpLabel", "acpLabel",
label = "Label :", label = "Label :",
choices = c( choices = c("..." = 0, sample_variables(data16S()))
"..." = 0,
sample_variables(data16S())
)
), ),
selectInput( selectInput(
"acpCol", "acpCol",
......
...@@ -7,174 +7,173 @@ shinyUI(dashboardPage( ...@@ -7,174 +7,173 @@ shinyUI(dashboardPage(
selectInput( selectInput(
"demo", "demo",
label = "Select demo data", label = "Select demo data",
choices = list( choices = list("Input data" = "input",
"Input data" = "input", "Chaillou et al., 2015" = "food"#,
"Chaillou et al., 2015" = "food"#, # "Mach et al., 2015" = "kinetic",
# "Mach et al., 2015" = "kinetic", # "Morton et al., 2017" = "soil",
# "Morton et al., 2017" = "soil", # "Ravel et al., 2011" = "ravel",
# "Ravel et al., 2011" = "ravel", #"GlobalPatterns" = "GlobalPatterns",
#"GlobalPatterns" = "GlobalPatterns", #"biorare"),
#"biorare" selected = 1
), )
selected = 1
)
),
hr(width = "90%"),
tags$div(
title = "Fichier d'abondance au format BIOM produit avec FROGS avec 'FROGS BIOM to std BIOM'",
fileInput(
"fileBiom",
label = h4("Fichier d'abondance :"),
placeholder = "data.biom"
), ),
radioButtons( hr(width = "90%"),
"biomFormat", tags$div(
label = NULL, title = "Fichier d'abondance au format BIOM produit avec FROGS avec 'FROGS BIOM to std BIOM'",
inline = TRUE, fileInput(
choices = list(`STD BIOM` = "std", "fileBiom",
`FROGS BIOM` = "frogs"), label = h4("Fichier d'abondance :"),
selected = "std" placeholder = "data.biom"
) ),
), radioButtons(
tags$div( "biomFormat",
style = "text-align:center", label = NULL,
title = "Rarefier les données avec un tirage aléatoire pour supprimer l'effet de la profondeur de séquençage", inline = TRUE,
checkboxInput("rareData", label = "Rarefier les donnees.", value = TRUE), choices = list(`STD BIOM` = "std",
textOutput("rarefactionMin") `FROGS BIOM` = "frogs"),
), selected = "std"
tags$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( tags$div(
"Histo global", style = "text-align:center",
plotOutput("histo", height = 700), title = "Rarefier les données avec un tirage aléatoire pour supprimer l'effet de la profondeur de séquençage",
uiOutput("histUI") checkboxInput("rareData", label = "Rarefier les donnees.", value = TRUE),
textOutput("rarefactionMin")
), ),
tabPanel( tags$div(
"Histo selectif", 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.",
plotOutput("histoFocus", height = 700), fileInput(
box( "fileMeta",
title = "Paramètres", label = h4("Metadata :"),
width = NULL, placeholder = "data.csv"
status = "primary",
uiOutput("histFocusUIfocusRank"),
uiOutput("histFocusUIfocusTaxa"),
uiOutput("histFocusUIfocusNbTaxa"),
uiOutput("histFocusUIfocusGrid"),
uiOutput("histFocusUIfocusX")
) )
), ),
tabPanel( radioButtons(
"Clustering", "CSVsep",
plotOutput("clust", height = 700), label = "CSV Séparateur",
uiOutput("clustUI") inline = TRUE,
choices = list(
`<tab>` = "\t",
`,` = ",",
`;` = ";",
excel = "excel"
)
), ),
tabPanel("Richesse alpha", box( tags$div(
width = NULL, tabsetPanel( title = "Arbre phylogéniques des OTU enracinné",
tabPanel( fileInput(
"Courbes", "fileTree",
plotOutput("richnessA", height = 700), label = h4("Arbre :"),
uiOutput("richnessAUI") placeholder = "data.nwk"
),
tabPanel("Tables", uiOutput("richnessATable"))
) )
)), )#,
tabPanel( # tags$div(
"Richesse beta", # title = "Séquences FASTA des OTU",
selectInput( # fileInput(
"richnessBDist", # "fileSeq",
label = "Distance :", # label = h4("Séquences de references :"),
choices = list( # placeholder = "data.fasta"
"bray", # )
"jaccard", # )
"unifrac", ),
"wunifrac", dashboardBody(
"dpcoa", tabsetPanel(
"jsd", tabPanel(
"euclidean" "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(
tabPanel( "Clustering",
"Heatmap", plotOutput("clust", height = 700),
plotOutput("richnessB", height = 700), uiOutput("clustUI")
uiOutput("richnessBUI") ),
), tabPanel("Richesse alpha", box(
tabPanel( width = NULL, tabsetPanel(
"Networks", tabPanel(
plotOutput("networkB", height = 700), "Courbes",
uiOutput("networkBUI") 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")) box(width = NULL, tabsetPanel(
)) tabPanel(
), "Heatmap",
tabPanel( plotOutput("richnessB", height = 700),
"Courbe de rarefaction", uiOutput("richnessBUI")
plotOutput("rarefactionCurve", height = 700), ),
uiOutput("rarefactionCurveUI") tabPanel(
), "Networks",
tabPanel( plotOutput("networkB", height = 700),
"Arbre phylo", uiOutput("networkBUI")
plotOutput("tree", height = 700), ),
uiOutput("treeUI") tabPanel("Tables", uiOutput("richnessBTable"))
), ))
tabPanel( ),
"Heatmap", tabPanel(
plotOutput("Heatmap", height = 700), "Courbe de rarefaction",
uiOutput("HeatmapUI") plotOutput("rarefactionCurve", height = 700),
), uiOutput("rarefactionCurveUI")
tabPanel( ),
"Analyses multivariées", tabPanel(
plotOutput("acp", height = 700), "Arbre phylo",
uiOutput("acpUI") plotOutput("tree", height = 700),
), uiOutput("treeUI")
tabPanel( ),
"et plus ...", tabPanel(
div( "Heatmap",
"Merci d'adresser vos remarques, bugs, demandes, besoins et conseils à ", plotOutput("Heatmap", height = 700),
a(href = "mailto:cedric.midoux@irstea.fr?subject=[Easy16S]", "cedric.midoux@irstea.fr") 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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