Commit 9193ac46 authored by Stevenn Volant's avatar Stevenn Volant
Browse files

correction heatmap

parent b4e394fd
......@@ -1011,6 +1011,7 @@ CheckCountsTable <- function(counts)
VarInt = input$VisuVarInt
ind_taxo = input$selectTaxoPlot
GetDataToPlot(resDiff,VarInt,ind_taxo,aggregate=FALSE)
tmp_merge = GetDataToPlot(resDiff,VarInt,ind_taxo,aggregate=FALSE)
counts_tmp_combined = tmp_merge$counts
......@@ -1333,7 +1334,7 @@ dataTmp = data.frame(value=c(alpha,beta,gamma),
rownames(log2FC) = rownames(result[[SelContrast[1]]])
rownames(padj) = rownames(result[[SelContrast[1]]])
return(list(log2FC=log2FC,padj=padj))
return(list(log2FC=as.data.frame(log2FC),padj=padj))
}
......@@ -1342,11 +1343,12 @@ dataTmp = data.frame(value=c(alpha,beta,gamma),
res = NULL
SelContrast = input$ContrastList_table_FC
log2FC = Get_log2FC_padj(input,BaseContrast,resDiff, info = NULL)$log2FC
cont = which(SelContrast%in%colnames(log2FC))
log2FC = log2FC[,cont]
if(!is.null(log2FC))
if(!is.null(log2FC) && length(SelContrast)>=2)
{
cont = which(colnames(log2FC)%in%SelContrast)
log2FC = log2FC[,SelContrast]
ind_taxo = input$selectTaxoPlot
ind = rownames(log2FC)%in%ind_taxo
log2FC = log2FC[ind,]
......
......@@ -1328,7 +1328,7 @@ output$RunButton <- renderUI({
res=NULL
if(input$PlotVisuSelect=="Barplot") res = showOutput("PlotVisuBar")
if(input$PlotVisuSelect=="Heatmap") res = d3heatmapOutput("heatmap", height = input$heightVisu+10)
if(input$PlotVisuSelect=="Boxplot") res = plotOutput("Boxplot", height = input$heightVisu+10)
if(input$PlotVisuSelect=="Boxplot") res = plotOutput("Boxplot", height = input$heightVisu+10)
if(input$PlotVisuSelect=="Diversity") res = plotOutput("DiversityPlot", height = input$heightVisu+10)
if(input$PlotVisuSelect=="Rarefaction") res = plotOutput("RarefactionPlot",dblclick = "RarefactionPlot_dblclick",brush = brushOpts(id = "RarefactionPlot_brush",resetOnNew = TRUE), height = input$heightVisu+10)
......
if(!require(shinydashboard)){
install.packages('shinydashboard')
library(shinydashboard)
......@@ -402,7 +403,7 @@ body <- dashboardBody(
tabItem(tabName = "Visu",
fluidRow(
column(width=9,
uiOutput("plotVisu")
uiOutput("plotVisu")
),
column(width=3,
......@@ -510,7 +511,7 @@ body <- dashboardBody(
## HEATMAP
##################
conditionalPanel(condition="input.PlotVisuSelect=='Heatmap' && input.HeatMapType!='Log2FC'",
selectInput("colors", label=h6(strong("Gradient of colors")),choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green"))
selectInput("colors", label=h6(strong("Gradient of colors")),choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green"),selected = "blue-white-red")
),
conditionalPanel(condition="input.PlotVisuSelect=='Heatmap'",
fluidRow(
......@@ -568,260 +569,6 @@ body <- dashboardBody(
)
)
# column(width=3,infoBoxOutput("NumberColBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberRowBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberQuantiBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberQualiBox",width=NULL))
# ),
# fluidRow(
#
# column(9,
# box(title = "Table de données", width = NULL, status = "success", solidHeader = TRUE,
# dataTableOutput("DataBrutes")
# )
# ),
# column(width=3,
# box(title = "Libéllés", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# h5(strong('Votre fichier contient t-il ...')),
# radioButtons('header', h5(strong('... des entêtes de colonnes ?')),choices=list("Oui" = 1,"Non" = 0),selected=1),
# radioButtons('rnames', h5(strong('... des libellés de ligne ?')),choices=list("Oui" = 1,"Non" = 0),selected=1)
# ),
#
# box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# column(width=3,infoBoxOutput("NumberColBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberRowBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberQuantiBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberQualiBox",width=NULL))
# ),
# fluidRow(
#
# column(9,
# box(title = "Table de données", width = NULL, status = "success", solidHeader = TRUE,
# dataTableOutput("DataBrutes")
# )
# ),
# column(width=3,
# box(title = "Libéllés", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# h5(strong('Votre fichier contient t-il ...')),
# radioButtons('header', h5(strong('... des entêtes de colonnes ?')),choices=list("Oui" = 1,"Non" = 0),selected=1),
# radioButtons('rnames', h5(strong('... des libellés de ligne ?')),choices=list("Oui" = 1,"Non" = 0),selected=1)
# ),
#
# box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# column(width=3,infoBoxOutput("NumberColBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberRowBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberQuantiBox",width=NULL)),
# column(width=3,infoBoxOutput("NumberQualiBox",width=NULL))
# ),
# fluidRow(
#
# column(9,
# box(title = "Table de données", width = NULL, status = "success", solidHeader = TRUE,
# dataTableOutput("DataBrutes")
# )
# ),
# column(width=3,
# box(title = "Libéllés", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# h5(strong('Votre fichier contient t-il ...')),
# radioButtons('header', h5(strong('... des entêtes de colonnes ?')),choices=list("Oui" = 1,"Non" = 0),selected=1),
# radioButtons('rnames', h5(strong('... des libellés de ligne ?')),choices=list("Oui" = 1,"Non" = 0),selected=1)
# ),
#
# box(title = "Choix des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# uiOutput("SelectDataVar"),
# actionButton("RefreshData",icon=icon("refresh"),strong("Actualiser"))
# ),
#
# box(title = "Transformer des variables", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
# uiOutput("SelectVarQuanti"),
# actionButton("GoQuali",icon=icon("arrow-circle-right"),strong("Transformer")),
# uiOutput("QuantiToQuali"))
# )
# )
#
# ),
# tabItem(tabName = "AnaStat",
#
# p("De nombreuses analyses statistiques peuvent être réalisées à partir de vos données. Decouvrez l'information
# contenue dans vos données (analyse unvariée) et étudier les relations entre vos différentes variables.")
# ),
#
# tabItem(tabName = "DescGene",
# fluidRow(
#
# column(width=9,
# tabBox(side = "left",id = 'tabs', width=NULL, status = "primary",
# tabPanel("Variables quantitatives",value=1,
# h4(strong("Statistiques descriptives (variables quantitatives)")),
# dataTableOutput("TableQuanti")
#
# ),
# tabPanel("Variables qualitatives",value=2,
# h4(strong("Statistiques descriptives (variables qualitatives)")),
# dataTableOutput("TableQuali")
# ),
# tabPanel("Table des corrélations",value=3,
# h4(strong("Table des corrélations")),
# dataTableOutput("CorTable")
# )
#
#
# ),
#
# conditionalPanel(condition="input.TestCor==true",
# box(title="Résultat du test",width = NULL, status = "success", solidHeader = TRUE,collapsible = TRUE,
# dataTableOutput("CorTableTest")
#
#
# ))
# ),
# column(width=3,
# box(title = "Choix de l'analyse", width = NULL, status = "primary", solidHeader = TRUE,
# conditionalPanel(condition = "input.tabs==1",
# selectInput("IndicQuanti",p(strong("Choisissez les indicateurs"),h6(em("Sélection multiple avec CTRL"))),
# c("Nb valeurs"=1,
# "Nb manquants"=2,
# "Somme"=3,
# "Min"=4,
# "1er Quartile"=5,
# "Mediane"=6,
# 'Moyenne'=7,
# "3eme Quartile"=8,
# "Max"=9,
# "Variance"=10,
# "Ecart-type"=11,
# "Coeff Variation"=12),
# selected=c(1,2,3,4,5,6,7,10),multiple=TRUE,size=2,selectize=FALSE),
# actionButton("RefreshStat",icon=icon("refresh"),strong("Refresh"))
# ),
# conditionalPanel(condition = "input.tabs==2",
# selectInput("IndicQuali",p(strong("Choisissez les indicateurs"),h6(em("Sélection multiple avec CTRL"))),
# c("Effectifs"=1,
# "%"=2,
# "% cumulés"=3),
# selected=c(1,2,3),multiple=TRUE,size=2,selectize=FALSE),
# actionButton("RefreshStatQuali",icon=icon("refresh"),strong("Refresh"))
# ),
#
# conditionalPanel(condition = "input.tabs==3",
# radioButtons("CorelMeth","Choix de la corrélation",
# choices=c("Pearson"="pearson","Spearman"="spearman","Kendall"="kendall")),
# checkboxInput("TestCor","Test de corrélation",value=FALSE)
# )
# ),
# box(title = "Aide", width = NULL, status = "warning", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE
# )
# )
# )
# ),
#
# tabItem(tabName = "AnalUni",
# fluidRow(
# column(width = 9,
# box(
# title = "Représentation",status = "success", solidHeader = TRUE,collapsible = TRUE,width=NULL,
# plotOutput("plotuni"),
# p(Align='right',
# downloadButton("exportPDFuni", "Download pdf"),
# downloadButton("exportPNGuni", "Download png")
# )
# ),
# conditionalPanel(condition="input.TestMoyCible==true", infoBoxOutput("ResTTestBox",width=6))
# ),
# column(width = 3,
# box(
# title = "Choix de l'analyse", width = NULL, status = "primary", solidHeader = TRUE,
#
# uiOutput("SelectUniVar"),
# uiOutput("RadioUniPlot"),
# checkboxInput("TestMoyCible","T-test",value=FALSE),
# conditionalPanel(condition="input.TestMoyCible==true",
# textInput("ValCibleTtest", label ="Valeur cible", value = 0,width="50%"),
# textInput("alphaTtest", label ="Seuil (en %)", value = 5,width="50%"),
# actionButton("ExecuteTtestCible",icon=icon("sign-in"),strong("Exécuter"))
# )
# ),
# box(
# title = "Options du graphique", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#
# conditionalPanel(condition="input.RadioPlotUni=='BarPlot'",sliderInput("widthBarPlot", "Taille des barres",min=1, max=100, value=50, step=1)),
# conditionalPanel(condition="input.RadioPlotUni=='Pie'", sliderInput("PieWidth", "Largeur", min=1, max=100, value=100, step=1)),
# conditionalPanel(condition="input.RadioPlotUni!='Pie'", sliderInput("SizeQQplot", "Taille",min=1, max=10, value=2, step=0.5)),
#
# selectInput("ColorUniplot", "Couleur",choices=c("Bleue" = 'blue',"Rouge"='red',"Vert"='green', "Noir"='black'),width="50%"),
# sliderInput("TransAlphaUni", "Transparence",min=1, max=100, value=50, step=1),
# conditionalPanel(condition="input.RadioPlotUni=='hist'",sliderInput("binwidth", "Taille de la fenètre glissante",min=1, max=100, value=1, step=1)),
# conditionalPanel(condition="input.RadioPlotUni=='hist'", radioButtons("HistDens","Ordonnées",choices=c("Comptages"="counts","Fréquences"="freq"))),
# conditionalPanel(condition="input.RadioPlotUni=='hist'", checkboxInput("CheckDens","Ajouter la densité",value=FALSE)),
# conditionalPanel(condition="input.RadioPlotUni!='qqplot'", radioButtons("SensGraph","Sens du graph",choices=c("Vertical"="Vert","Horizontal"="Hori"))),
# conditionalPanel(condition="input.RadioPlotUni=='box'", checkboxInput("CheckAddPointsBox","Ajouter les données",value=FALSE)),
# conditionalPanel(condition="input.RadioPlotUni=='BarPlot'",checkboxInput("BarCircular","Représentation circulaire",FALSE))
#
# )
# )
# )
#
#
#
# ),
#
# tabItem(tabName = "AnalBi",
#
# fluidRow(
# column(width=9,
# box(
# title = "Représentation", width = NULL, status = "success", solidHeader = TRUE,collapsible = TRUE,
#
# plotOutput("biplot",
# dblclick = dblclickOpts(
# id = "biplot_dblclick"
# ),
# hover = hoverOpts(
# id = "biplot_hover"
# ),
# brush = brushOpts(
# id = "biplot_brush",
# resetOnNew = TRUE
# )
# ),
# p(Align='right',
# downloadButton("exportPDFbi", "Download pdf"),
# downloadButton("exportPNGbi", "Download png")
# )
# ),
# conditionalPanel(condition="input.TestMoy==true", infoBoxOutput("ResTTest2sampBox",width=6)),
# conditionalPanel(condition="input.RadioPlotBi=='Nuage'",infoBoxOutput("biplot_info",width=6))
# ),
# column(width=3,
# box(
# title = "Choix de l'analyse", width = NULL, status = "primary", solidHeader = TRUE,
#
# uiOutput("SelectDataVarBi1"),
# uiOutput("SelectDataVarBi2"),
# uiOutput("RadioBiPlot"),
# uiOutput("CheckTestBi"),
# conditionalPanel(condition="input.TestBi!=''",textInput("alphaTtestMoy", label ="Seuil (en %)", value = 5,width="50%")),
# conditionalPanel(condition="input.RadioPlotBi=='Nuage'", h5(strong("Modèle linéaire")),checkboxInput("CheckLM", "Droite de régression",value = FALSE))
#
# ),
# box(
# title = "Options du graphique", width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
#
# sliderInput("SizePoint", "Taille",min=1, max=10, value=2, step=0.5),
# conditionalPanel(condition="input.RadioPlotBi=='hist'",sliderInput("binwidthBi", "Taille de la fenètre glissante",min=1, max=100, value=1, step=1)),
# 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"))),
# conditionalPanel(condition="input.RadioPlotBi=='box'", checkboxInput("CheckAddPointsBoxBi","Ajouter les données",value=FALSE))
#
# )
#
# )
#
#
#
# )
)
......
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