"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'.\nVous pouvez egalement choisir un dataset de demo"
"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"
title="Metadata table with variables (in columns) and samples (in rows). \nMake sure you follow the exact spelling of the sample names (1st column). \nThe import of an excel table is possible but not recommended.",
fileInput("fileMeta",
label="Metadata table : ",
placeholder="data.csv")
),
radioButtons(
"CSVsep",
label="CSV separator : ",
inline=TRUE,
choices=list(
`<tab>`="\t",
`,`=",",
`;`=";",
excel="excel"
)
),
tags$div(
title="Phylogenetic tree",
fileInput("fileTree",
label="Phylogenetic tree : ",
placeholder="data.nwk")
)#,
# tags$div(
# title = "Representative FASTA sequences of OTU",
# fileInput(
# "fileSeq",
# label = "FASTA sequences : "),
# placeholder = "data.fasta"
# )
# )
),
dashboardBody(
tabsetPanel(
tabPanel(
"Summary",
verbatimTextOutput("phyloseqPrint"),
uiOutput("summaryTable")
),
),
tags$div(
tabPanel(
style="text-align:center",
"Global barplot",
title="Rarefier les données avec un tirage aléatoire pour supprimer l'effet de la profondeur de séquençage",
plotOutput("histo",height=700),
checkboxInput("rareData",label="Rarefier les donnees.",value=TRUE),
uiOutput("histUI")
textOutput("rarefactionMin")
),
),
tags$div(
tabPanel(
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.",
"Focus barplot",
fileInput(
plotOutput("histoFocus",height=700),
"fileMeta",
box(
label=h4("Metadata :"),
title="Paramètres",
placeholder="data.csv"
width=NULL,
status="primary",
uiOutput("histFocusUIfocusRank"),
uiOutput("histFocusUIfocusTaxa"),
uiOutput("histFocusUIfocusNbTaxa"),
uiOutput("histFocusUIfocusGrid"),
uiOutput("histFocusUIfocusX")
)
)
),
),
radioButtons(
tabPanel(
"CSVsep",
"Clustering",
label="CSV Séparateur",
plotOutput("clust",height=700),
inline=TRUE,
uiOutput("clustUI")
choices=list(
`<tab>`="\t",
`,`=",",
`;`=";",
excel="excel"
)
),
),
tags$div(
tabPanel(HTML("α-diversity"),
title="Arbre phylogéniques des OTU enracinné",
box(
fileInput(
width=NULL,tabsetPanel(
"fileTree",
tabPanel(
label=h4("Arbre :"),
"Plots",
placeholder="data.nwk"
plotOutput("richnessA",height=700),
)
uiOutput("richnessAUI")
)#,
),
# tags$div(
tabPanel("Tables",uiOutput("richnessATable"))
# title = "Séquences FASTA des OTU",
)
# fileInput(
)),
# "fileSeq",
tabPanel(
# label = h4("Séquences de references :"),
HTML("β-diversity"),
# placeholder = "data.fasta"
selectInput(
# )
"richnessBDist",
# )
label="Distance : ",
),
choices=list(
dashboardBody(
"bray",
tabsetPanel(
"jaccard",
tabPanel(
"unifrac",
"Summary",
"wunifrac",
verbatimTextOutput("phyloseqPrint"),
"dpcoa",
uiOutput("summaryTable")
"jsd",
),
"euclidean"
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(
box(width=NULL,tabsetPanel(
"Clustering",
tabPanel(
plotOutput("clust",height=700),
"Heatmap",
uiOutput("clustUI")
plotOutput("richnessB",height=700),
),
uiOutput("richnessBUI")
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"
)
),
),
box(width=NULL,tabsetPanel(
tabPanel(
tabPanel(
"Networks",
"Heatmap",
plotOutput("networkB",height=700),
plotOutput("richnessB",height=700),
uiOutput("networkBUI")
uiOutput("richnessBUI")
),
),
tabPanel("Tables",uiOutput("richnessBTable"))
tabPanel(
))
"Networks",
),
plotOutput("networkB",height=700),
tabPanel(
uiOutput("networkBUI")
"Rarefaction curves",
),
plotOutput("rarefactionCurve",height=700),
tabPanel("Tables",uiOutput("richnessBTable"))
uiOutput("rarefactionCurveUI")
))
),
),
tabPanel(
tabPanel(
"Phylogenetic tree",
"Courbe de rarefaction",
plotOutput("tree",height=700),
plotOutput("rarefactionCurve",height=700),
uiOutput("treeUI")
uiOutput("rarefactionCurveUI")
),
),
tabPanel(
tabPanel(
"Heatmap",
"Arbre phylo",
plotOutput("Heatmap",height=700),
plotOutput("tree",height=700),
uiOutput("HeatmapUI")
uiOutput("treeUI")
),
),
tabPanel(
tabPanel(
"MultiDimensional Scaling",
"Heatmap",
plotOutput("acp",height=700),
plotOutput("Heatmap",height=700),
uiOutput("acpUI")
uiOutput("HeatmapUI")
),
),
tabPanel(
tabPanel(
"News features ...",
"Analyses multivariées",
div(
plotOutput("acp",height=700),
"Questions, problems or comments regarding this application should be sent to ",
