Commit 04901d36 authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Last modif stevenn

parent b72cdb5a
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......@@ -2,6 +2,14 @@
library(shinydashboard)
library(DT)
library(biom)
library(DESeq2)
library(rNVD3)
library(RColorBrewer)
library(gplots)
library(ggdendro)
library(dendextend)
library(circlize)
library(ade4)
sidebar <- dashboardSidebar(
sidebarMenu(
......@@ -27,10 +35,10 @@ body <- dashboardBody(
fluidRow(
column(12,
h3(strong("Instructions")),
p("Décrire le format des différents fichiers"),
p("Décrire le format des différents fichiers"),
p("Décrire le format des différents fichiers"),
p("Décrire le format des différents fichiers")
p("Provide the input data")
# p("Décrire le format des différents fichiers"),
# p("Décrire le format des différents fichiers"),
# p("Décrire le format des différents fichiers")
),
br(),
......@@ -47,8 +55,8 @@ body <- dashboardBody(
),
box(title="Load the taxonomy file",width = 4, status = "primary", solidHeader = TRUE,collapsible = FALSE,
radioButtons("TypeTaxo",h6(strong("Format:")),c("Table"="Table","RDP"="RDP")),
fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
)
),
......@@ -92,8 +100,9 @@ body <- dashboardBody(
column(width=6,uiOutput("SelectInteraction2")),
column(width=6,actionButton("RunDESeq",strong("Run analysis"),icon = icon("caret-right")))
)
)
),
uiOutput("BoxTarget"),
uiOutput("BoxCountsMerge")
),
column(width=7,
......@@ -114,7 +123,7 @@ body <- dashboardBody(
),
fluidRow(
column(width=3,
radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='NULL',"No cut-off"=Inf,"Value"="val")),
radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='Auto',"No cut-off"=Inf,"Value"="val")),
conditionalPanel(condition="input.CooksCutOff=='val'",textInput("CutOffVal",h6("Cut-off:"),value=0))
),
......@@ -124,58 +133,81 @@ body <- dashboardBody(
column(width=3,
radioButtons("fitType",h6(strong("Relationship")),choices = c("Parametric"="parametric","Local"="local"))
),
column(width=3,
conditionalPanel(condition="input.FileFormat=='fileCounts' && input.TypeTaxo=='RDP'",
sliderInput("ThreshProba",h6(strong("Probability threshold (rdp annotation)")),min=0.01, max=1,value=0.5,step = 0.01)
)
),
column(width=3,uiOutput("RefSelect"))
)
),
uiOutput("BoxTarget")
)
),
fluidRow(
column(width=12,
box(title="Contrasts",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
column(width=3,uiOutput("contrastMat")),
column(width=3,
textInput("ContrastName","Contrast name","Name..."),
actionButton("AddContrast","Add contrast",icon = icon("plus"))
textInput("ContrastName","Contrast name","Name..."),
actionButton("AddContrast","Add contrast",icon = icon("plus"))
),
column(width=3,
selectInput("ContrastList","Contrasts","",multiple=TRUE,size=2,selectize=FALSE),
actionButton("RemoveContrast","Remove",icon = icon("remove"))
selectInput("ContrastList","Contrasts","",multiple=TRUE,size=2,selectize=FALSE),
actionButton("RemoveContrast","Remove",icon = icon("remove"))
),
column(width=3,
h5(strong("Selected contrast:")),
htmlOutput("ContrastOverview")
h5(strong("Selected contrast:")),
htmlOutput("ContrastOverview")
)
)
)
)
)
# fluidRow(
# column(width=12,
#
# )
# )
),
tabItem(tabName = "DiagPlot",
tabItem(tabName = "DiagPlotTab",
fluidRow(
column(width=9,
box(title = "Plot", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
plotOutput("PlotDiag"),
p(Align='right',
downloadButton("exportPDFdiag", "Download pdf"),
downloadButton("exportPNGdiag", "Download png")
)
plotOutput("PlotDiag")
),
br(),
conditionalPanel(condition="input.DiagPlot=='Sfactors'",
box(title = "Size factors", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
dataTableOutput("SizeFactTable")
)
),
conditionalPanel(condition="input.DiagPlot=='pcaPlot'",
box(title = "Eigen values", width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
plotOutput("PlotEigen")
)
),
conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
box(title = "Eigen values", width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
plotOutput("PlotpcoaEigen")
)
)
),
column(width=3,
box(
title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
selectInput("DiagPlot",h6(strong("Select the plot")),c("Total barplot"="barplotTot","Nul barplot"="barplotNul","Maj. taxonomy"="MajTax", "Density"="densityPlot","Size factors"="Sfactors", "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot")),
conditionalPanel(condition="input.DiagPlot!='pcaPlot' && input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntBarPlot"))
box(title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
selectInput("DiagPlot",h6(strong("Select the plot")),c("Total barplot"="barplotTot","Nul barplot"="barplotNul",
"Maj. taxonomy"="MajTax", "Density"="densityPlot","Size factors"="Sfactors",
"Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","Clustering" = "clustPlot",
"SERE" = "SERE")),
conditionalPanel(condition="input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntDiag")),
conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
h5(strong("Select the modalities")),
uiOutput("ModMat"),
selectInput("DistPCOA","Distance",c("euclidean", "canberra", "bray", "kulczynski", "jaccard",
"gower", "altGower", "morisita", "horn","mountford","raup","binomial",
"chao","cao","mahalanobis"),selected="jaccard")
),
downloadButton("exportPDFdiag", "Download pdf"),
downloadButton("exportPNGdiag", "Download png")
# conditionalPanel(condition="input.RadioPlotBi=='Nuage'",selectInput("ColorBiplot", "Couleur",choices=c("Bleue" = 'blue',"Rouge"='red',"Vert"='green', "Noir"='black'),width="50%")),
# sliderInput("TransAlphaBi", "Transparence",min=1, max=100, value=50, step=1),
# conditionalPanel(condition="input.RadioPlotBi!='Nuage'", radioButtons("SensGraphBi","Sens du graph",choices=c("Vertical"="Vert","Horizontal"="Hori"))),
......@@ -186,7 +218,23 @@ body <- dashboardBody(
conditionalPanel(condition="input.DiagPlot=='Sfactors'",
h6(strong("Layout")),
numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
)
),
conditionalPanel(condition="input.DiagPlot=='clustPlot'",
h6(strong("Layout")),
selectInput("typeHculst", h6("Type"),c("Horizontal"="hori","Fan"="fan")),
checkboxInput("colorHC","Add color",value=TRUE)
),
conditionalPanel(condition="input.DiagPlot=='pcoaPlot'", selectInput("labelPCOA","Label type",c("Group", "Sample"),selected="Group"),
#checkboxInput("colorgroup","Same color for the group",value=FALSE),
sliderInput("cexcircle", "Circle size",min=0,max=2,value = 0.9,step =0.1),
sliderInput("cexpoint", "Point size",min=0,max=3,value = 1,step =0.1),
sliderInput("cexstar", "Star height",min=0,max=1,value = 0.95,step =0.1)
),
sliderInput("cexLabelDiag", "Label size",min=0,max=5,value = 1,step =0.1)
# sliderInput("heightDiag", "height",min=100,max=1500,value = 500,step =10),
# sliderInput("widthDiag", "width",min=100,max=1500,value = 1000,step =10)
)
)
......@@ -194,19 +242,160 @@ body <- dashboardBody(
),
tabItem(tabName = "TableDiff",
fluidRow(
column(width=3,p("Table of differential abundance"))
)
column(width=9,uiOutput("TabBoxDataDiff")),
column(width=3,
box(title = "Select your contrast", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
selectInput("ContrastList_table",h6(strong("Contrast list")),"", multiple = FALSE),
htmlOutput("ContrastOverviewTable")
)
)
)
),
#### Data Viz
tabItem(tabName = "Visu",
tabItem(tabName = "BarplotVisu",
fluidRow(
column(width=3,p("Visualisation"))
)
column(width=9,showOutput("PlotVisu")),
column(width=3,
box(title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
uiOutput("VarIntVisuBP"),
uiOutput("TaxoToPlotBP"),
radioButtons(inputId = "CountsOrProp",label = "Value: ",choices = c("Proportions" = "prop", "Counts" = "counts"),selected = "prop"),
radioButtons(inputId = "SensPlotVisuBP",label = "Type: ",choices = c("Vertical" = "multiBarChart", "Horizontal" = "multiBarHorizontalChart"),selected = "multiBarChart")
),
box(title = "Appearance", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
sliderInput("heightVisu", h6(strong("Height")),min=100,max=2000,value = 800),
sliderInput("widthVisu", h6(strong("Width")),min=100,max=1200,value = 1000)
)
)
)
),
tabItem(tabName = "HeatmapVisu",
fluidRow(
column(width=9,
#d3heatmapOutput(outputId ='d3heatmap', width = "1000p", height = "800px")
plotOutput("heatmap")
),
# downloadButton("exportPDFVisu", "Download pdf"),
# downloadButton("exportPNGVisu", "Download png")
#)
column(width=3,
box(title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
selectInput(inputId = "HeatMapType",label = h6(strong("Data")),choices = c("Counts" = "Counts", "Log2FC" = "Log2FC"),selected = "Counts"),
selectInput("ContrastList_table_FC",h6(strong("Contrast list")),"", multiple = TRUE),
uiOutput("VarIntVisuHM"),
uiOutput("TaxoToPlotHM"),
radioButtons(inputId = "SensPlotVisuHM",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical"),
selectInput(inputId = "scaleHeatmap",label = h6(strong("Scale:")),choices = c("None" = "none", "Rows" = "row", "Column" = "col"),selected = "none")
),
box(title = "Appearance", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
sliderInput("heightHeat", h6(strong("Height")),min=100,max=2000,value = 800),
sliderInput("LabelSizeHeatmap", h6(strong("Label size")),min=0.1,max=2,value = 0.7,step = 0.1)
)
)
)
),
tabItem(tabName = "BoxplotVisu",
fluidRow(
column(width=9,plotOutput("Boxplot"), uiOutput("BoxCountsMerge_pierre")),
# downloadButton("exportPDFVisu", "Download pdf"),
# downloadButton("exportPNGVisu", "Download png")
#)
column(width=3,
box(title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
uiOutput("VarIntVisuBoxP"),
uiOutput("TaxoToPlotBoxP"),
selectInput("typeDataBox","Type of data",c("Log2"="Log2","Relative"="Relative")),
radioButtons(inputId = "SensPlotVisuBoxP",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical")
),
box(title = "Appearance", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
sliderInput("heightBoxP", h6(strong("Height")),min=100,max=2000,value = 800),
checkboxInput("CheckAddPointsBox","Add points",value=TRUE)
)
)
)
),
tabItem(tabName = "DiversityVisu",
fluidRow(
column(width=9,plotOutput("DiversityPlot")
# conditionalPanel(condition="input.AddBoxplotDiv==TRUE",
# plotOutput("DiversityBoxPlot")
# )
),
column(width=3,
box(title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
uiOutput("VarIntVisuDiv"),
selectizeInput("WhichDiv",h6(strong("Diversity")),c('Alpha','Beta','Gamma'),selected = c('Alpha','Beta','Gamma'),multiple=TRUE),
radioButtons(inputId = "SensPlotVisuGlobal",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical"),
checkboxInput("AddBoxplotDiv","AddBoxplot",value=FALSE),
conditionalPanel(condition="input.AddBoxplotDiv==TRUE",
uiOutput("SelectVarBoxDiv")
)
# uiOutput("DiversityGroupBy")
),
box(title = "Appearance", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
sliderInput("sizePointGlobal", h6(strong("Points size")),min=0.5,max=10,value =3,step=0.5),
checkboxInput("SplitVisuGlobal","Split diversity",value=FALSE)
)
)
)
),
tabItem(tabName = "RarefactionVisu",
fluidRow(
column(width=9,
plotOutput("RarefactionPlot",
dblclick = "RarefactionPlot_dblclick",
brush = brushOpts(
id = "RarefactionPlot_brush",
resetOnNew = TRUE
)
))
# column(width=3,
# box(title = "Options", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
# # uiOutput("VarIntVisuDiv"),
# # selectizeInput("WhichDiv",h6(strong("Diversity")),c('Alpha','Beta','Gamma'),selected = c('Alpha','Beta','Gamma'),multiple=TRUE),
# # radioButtons(inputId = "SensPlotVisuGlobal",label = "Type: ",choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical")
# #
# # # uiOutput("DiversityGroupBy")
# ),
# box(title = "Appearance", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# # #selectInput("colors", label="Gradient of colors:",choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green")),
# # sliderInput("sizePointGlobal", h6(strong("Points size")),min=0.5,max=5,value = 1.5,step=0.5),
# # checkboxInput("SplitVisuGlobal","Split diversity",value=FALSE)
# #
# )
# )
)
),
#### Krona plot
tabItem(tabName = "Krona",
fluidRow(
......
"C1" "C2"
0 0
1 1
-1 -1
"C1" "C2" "Name....4" "Name..." "Name....1" "Name....2" "Name....3" "Name..."
0 0 1 0 1 0 0 0
1 1 1 0 0 1 1 1
-1 -1 -1 0 0 -1 -12 -0.5
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product-home-product-home-account-end,1
home-product-product-home-account-end,1
search-search-home-product-account-end,1
home-product-home-account-home-end,2
search-product-home-account-home-end,1
home-home-product-account-home-end,2
account-home-account-home-home-end,1
home-home-home-home-home-end,6
product-home-home-home-home-end,3
product-other-home-home-home-end,1
search-other-home-home-home-end,1
home-product-home-home-home-end,3
product-product-home-home-home-end,1
home-search-home-home-home-end,1
search-search-home-home-home-end,1
home-home-other-home-home-end,1
product-product-other-home-home-end,1
search-product-other-home-home-end,1
home-home-product-home-home-end,1
other-home-product-home-home-end,2
product-home-product-home-home-end,1
home-product-product-home-home-end,2
product-product-product-home-home-end,3
product-home-account-other-home-end,1
other-account-home-product-home-end,1
product-account-home-product-home-end,1
home-home-home-product-home-end,2
search-other-home-product-home-end,1
product-product-home-product-home-end,2
product-search-other-product-home-end,1
product-home-product-product-home-end,2
home-product-product-product-home-end,1
product-search-product-product-home-end,1
home-home-home-search-home-end,1
home-product-home-search-home-end,3
home-product-other-search-home-end,1
home-product-home-account-other-end,3
home-home-home-home-other-end,1
home-product-home-home-other-end,2
home-product-product-home-other-end,1
home-home-home-product-other-end,1
home-home-home-search-other-end,1
home-home-account-account-product-end,1
search-home-product-account-product-end,1
home-home-home-home-product-end,5
product-home-home-home-product-end,2
search-home-home-home-product-end,1
home-search-home-home-product-end,1
product-search-home-home-product-end,1
account-other-product-home-product-end,1
product-product-product-home-product-end,1
product-home-search-home-product-end,1
home-search-home-other-product-end,1
home-product-home-product-product-end,1
home-home-other-product-product-end,1
product-home-other-product-product-end,1
product-home-home-search-product-end,2
home-product-home-search-product-end,1
product-home-product-search-product-end,1
home-product-product-search-product-end,1
other-account-home-home-search-end,1
search-home-home-home-search-end,2
home-other-home-home-search-end,1
search-product-home-home-search-end,1
product-product-product-home-search-end,1
product-product-home-product-search-end,1
home-product-search-product-search-end,1
home-search-search-product-search-end,1
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