ui.R 43.5 KB
Newer Older
Stevenn Volant's avatar
Stevenn Volant committed
1
2
3
4
5
if(!require(shinydashboard)){
  install.packages('shinydashboard')
  library(shinydashboard)
}

stevenn's avatar
stevenn committed
6
7
if (!require(psych)) {
  install.packages('psych')
Stevenn Volant's avatar
Stevenn Volant committed
8
  
stevenn's avatar
stevenn committed
9
  library(psych)
Stevenn Volant's avatar
Stevenn Volant committed
10
  
stevenn's avatar
stevenn committed
11
}
Stevenn Volant's avatar
Stevenn Volant committed
12

stevenn's avatar
stevenn committed
13
if (!require(ggplot2)) {
Stevenn Volant's avatar
Stevenn Volant committed
14
  
stevenn's avatar
stevenn committed
15
  install.packages('ggplot2')
Stevenn Volant's avatar
Stevenn Volant committed
16
  
stevenn's avatar
stevenn committed
17
  library(ggplot2)
Stevenn Volant's avatar
Stevenn Volant committed
18
  
stevenn's avatar
stevenn committed
19
}
Stevenn Volant's avatar
Stevenn Volant committed
20

stevenn's avatar
stevenn committed
21
if (!require(vegan)) {
Stevenn Volant's avatar
Stevenn Volant committed
22
  
stevenn's avatar
stevenn committed
23
  install.packages('vegan')
Stevenn Volant's avatar
Stevenn Volant committed
24
  
stevenn's avatar
stevenn committed
25
  library(vegan)
Stevenn Volant's avatar
Stevenn Volant committed
26
  
stevenn's avatar
stevenn committed
27
}
Stevenn Volant's avatar
Stevenn Volant committed
28

stevenn's avatar
stevenn committed
29
if (!require(dendextend)) {
Stevenn Volant's avatar
Stevenn Volant committed
30
  
stevenn's avatar
stevenn committed
31
  install.packages('dendextend')
Stevenn Volant's avatar
Stevenn Volant committed
32
  
stevenn's avatar
stevenn committed
33
  library(dendextend)
Stevenn Volant's avatar
Stevenn Volant committed
34
  
stevenn's avatar
stevenn committed
35
}
Stevenn Volant's avatar
Stevenn Volant committed
36

stevenn's avatar
stevenn committed
37
if (!require(circlize)) {
Stevenn Volant's avatar
Stevenn Volant committed
38
  
stevenn's avatar
stevenn committed
39
  install.packages('circlize')
Stevenn Volant's avatar
Stevenn Volant committed
40
  
stevenn's avatar
stevenn committed
41
  library(circlize)
Stevenn Volant's avatar
Stevenn Volant committed
42
  
stevenn's avatar
stevenn committed
43
}
Stevenn Volant's avatar
Stevenn Volant committed
44

stevenn's avatar
stevenn committed
45
if (!require(biom)) {
Stevenn Volant's avatar
Stevenn Volant committed
46
  
stevenn's avatar
stevenn committed
47
  install.packages('biom')
Stevenn Volant's avatar
Stevenn Volant committed
48
  
stevenn's avatar
stevenn committed
49
  library(biom)
Stevenn Volant's avatar
Stevenn Volant committed
50
  
stevenn's avatar
stevenn committed
51
}
Stevenn Volant's avatar
Stevenn Volant committed
52

stevenn's avatar
stevenn committed
53
if (!require(DT)) {
Stevenn Volant's avatar
Stevenn Volant committed
54
  
stevenn's avatar
stevenn committed
55
  install.packages('DT')
Stevenn Volant's avatar
Stevenn Volant committed
56
  
stevenn's avatar
stevenn committed
57
  library(DT)
Stevenn Volant's avatar
Stevenn Volant committed
58
  
stevenn's avatar
stevenn committed
59
}
Stevenn Volant's avatar
Stevenn Volant committed
60

stevenn's avatar
stevenn committed
61
if (!require(RColorBrewer)) {
Stevenn Volant's avatar
Stevenn Volant committed
62
  
stevenn's avatar
stevenn committed
63
  install.packages('RColorBrewer')
Stevenn Volant's avatar
Stevenn Volant committed
64
  
stevenn's avatar
stevenn committed
65
  library(RColorBrewer)
Stevenn Volant's avatar
Stevenn Volant committed
66
  
stevenn's avatar
stevenn committed
67
}
Stevenn Volant's avatar
Stevenn Volant committed
68

stevenn's avatar
stevenn committed
69
if (!require(gplots)) {
Stevenn Volant's avatar
Stevenn Volant committed
70
  
stevenn's avatar
stevenn committed
71
  install.packages('gplots')
Stevenn Volant's avatar
Stevenn Volant committed
72
  
stevenn's avatar
stevenn committed
73
  library(gplots)
Stevenn Volant's avatar
Stevenn Volant committed
74
  
stevenn's avatar
stevenn committed
75
}
Stevenn Volant's avatar
Stevenn Volant committed
76

stevenn's avatar
stevenn committed
77
if (!require(DESeq2)) {
Stevenn Volant's avatar
Stevenn Volant committed
78
  
stevenn's avatar
stevenn committed
79
  source("https://bioconductor.org/biocLite.R")
Stevenn Volant's avatar
Stevenn Volant committed
80
  
stevenn's avatar
stevenn committed
81
  biocLite("DESeq2")
Stevenn Volant's avatar
Stevenn Volant committed
82
  
stevenn's avatar
stevenn committed
83
  library(DESeq2)
Stevenn Volant's avatar
Stevenn Volant committed
84
  
stevenn's avatar
stevenn committed
85
}
Stevenn Volant's avatar
Stevenn Volant committed
86

stevenn's avatar
stevenn committed
87
if (!require(ade4)) {
Stevenn Volant's avatar
Stevenn Volant committed
88
  
stevenn's avatar
stevenn committed
89
  install.packages('ade4')
Stevenn Volant's avatar
Stevenn Volant committed
90
  
stevenn's avatar
stevenn committed
91
  library(ade4)
Stevenn Volant's avatar
Stevenn Volant committed
92
93
  
}
stevenn's avatar
stevenn committed
94
95

sidebar <- dashboardSidebar(
Stevenn Volant's avatar
Stevenn Volant committed
96
  
stevenn's avatar
stevenn committed
97
  sidebarMenu(
Stevenn Volant's avatar
Stevenn Volant committed
98
    
stevenn's avatar
stevenn committed
99
    menuItem("Home", tabName = "Home", icon = icon("home")),
Stevenn Volant's avatar
Stevenn Volant committed
100
    
101
    menuItem("Tutorial", tabName = "Tutorial", icon = icon("book")),
Stevenn Volant's avatar
Stevenn Volant committed
102
    
stevenn's avatar
stevenn committed
103
    menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
Stevenn Volant's avatar
Stevenn Volant committed
104
    
stevenn's avatar
stevenn committed
105
    menuItemOutput("dymMenu")
Stevenn Volant's avatar
Stevenn Volant committed
106
    
stevenn's avatar
stevenn committed
107
  )
Stevenn Volant's avatar
Stevenn Volant committed
108
  
stevenn's avatar
stevenn committed
109
110
111
)

body <- dashboardBody(
Stevenn Volant's avatar
Stevenn Volant committed
112
  
stevenn's avatar
stevenn committed
113
  tabItems(
Stevenn Volant's avatar
Stevenn Volant committed
114
    
stevenn's avatar
stevenn committed
115
    tabItem(tabName = "Home",
Stevenn Volant's avatar
Stevenn Volant committed
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
            
            tabBox(title="Welcome to Meta16S", id="tabset1", height = "700", width = 12,
                   
                   tabPanel("About", p("Meta16S is a web interface for the analysis of metagenomic data including the normalization,
                                       
                                       the differential analysis and mutiple visualization.",style = "font-family: 'times'; font-si16pt"),
                            
                            p("Meta16S is based on DESeq2 R package", a("[Anders and Huber 2010]", href="http://www.ncbi.nlm.nih.gov/pubmed/20979621"), "for the analysis of metagenomic data, as suggested in", a("[McMurdie and Holmes 2014]",href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/"),
                              
                              ". Meta16S robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2", a("[Love 2014]", href="http://www.ncbi.nlm.nih.gov/pubmed/25516281"),".
                              
                              Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995].
                              
                              The PCOA is performed with the", a("ade4 R package",href="http://pbil.univ-lyon1.fr/ade4/"), "and plots are generated with", a("ggplot2",href="http://ggplot2.org/"), "or", a("D3.js packages",href="http://d3js.org/"), ".", style = "font-family: 'times'; font-si16pt")),
                   
                   tabPanel("Authors", h3("The main contributors to Meta16s:"),
                            
                            p(a("Stevenn Volant", href="mailto:stevenn.volant@pasteur.fr"), "(Initiator, coding, testing, documentation, evaluation)"),
                            
                            p(a("Amine Ghozlane",href="mailto:amine.ghozlane@pasteur.fr"), "(Coding, testing, documentation, evaluation)"),
                            
                            p(a("Hugo Varet",href="mailto:hugo.varet@pasteur.fr"), "(Coding, testing, feature suggestions)"),
                            
                            p(a("Pierre Lechat",href="mailto:pierre.lechat@pasteur.fr"), "(Coding, testing, feature suggestions)"),
                            
                            p(a("Marie-Agnès Dillies",href="mailto:marie-agnes.dillies@pasteur.fr"), "(Evaluation)"),
                            
                            p(a("Sean Kennedy",href="mailto:sean.kennedy@pasteur.fr"), "(Evaluation)"),
                            
                            h3("Acknowledgements"),
                            
                            p("Thanks to the following people for patches and other suggestions for improvements:"),
                            
                            p(a("Christophe Malabat",href="mailto:christophe.malabat@pasteur.fr"))),
                   
                   tabPanel("Citing Meta16S",p("No papers about Meta16s have been published yet, but a manuscript is in preparation.",style = "font-family: 'times'; font-si16pt"),
                            
                            p("For now, if you have any comments, questions or suggestions, or want to use meta16s please contact", a("Dr. Marie-Agnès Dillies", href="mailto:marie-agnes.dillies@pasteur.fr"),".", style = "font-family: 'times'; font-si16pt; color:red"))
            ),
                   img(src = "logo.jpg", height = 90, width = 600,align="right")
    ),      

    
159
    tabItem(tabName = "Tutorial",
Stevenn Volant's avatar
Stevenn Volant committed
160
            
161
            h2("How to !")
Stevenn Volant's avatar
Stevenn Volant committed
162
            
163
    ),
Stevenn Volant's avatar
Stevenn Volant committed
164
    
stevenn's avatar
stevenn committed
165
166
167
    tabItem(tabName = "Upload",
            tags$style(type='text/css', ".well { max-width: 20em; }"),
            fluidRow(
Stevenn Volant's avatar
Stevenn Volant committed
168
169
170
171
172
173
174
              column(width=3,valueBoxOutput("valueErrorPercent",width=NULL)),
              column(width=3,infoBoxOutput("InfoErrorCounts",width=NULL)),
              column(width=3,infoBoxOutput("InfoErrorTaxo",width=NULL))
            ),
            br(),
             fluidRow(
                box(title="Select your file format",width = 3,status = "success", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
175
                  selectInput("FileFormat","",c("Counts table & taxonomy"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts")
Stevenn Volant's avatar
Stevenn Volant committed
176
                ),
stevenn's avatar
stevenn committed
177
                conditionalPanel(condition="input.FileFormat=='fileCounts'",
Stevenn Volant's avatar
Stevenn Volant committed
178
                  box(title="Load the counts table",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
179
                    fileInput('fileCounts', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
180
                  ),
stevenn's avatar
stevenn committed
181
                  
Stevenn Volant's avatar
Stevenn Volant committed
182
183
184
185
186
187
188
                  box(title="Load the taxonomy file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
                      fluidRow(
                        column(width=6,radioButtons("TypeTaxo",h6(strong("Format:")),c("Table"="Table","RDP"="RDP"))),
                        column(width=6,
                             conditionalPanel(condition="input.TypeTaxo=='RDP'",numericInput("RDP_th",h6(strong("Threshold:")),0.5,step=0.01,min=0.01,max=1))
                        )
                      ),
stevenn's avatar
stevenn committed
189
                      fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
190
191
192
193
194
                  )
                  
                ),
                
                conditionalPanel(condition="input.FileFormat=='fileBiom'",
Stevenn Volant's avatar
Stevenn Volant committed
195
                                 box(title="Load the BIOM file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
196
197
198
                                     fileInput('fileBiom', h5(strong('Select your file')),width="100%")
                                 )           
                )
Stevenn Volant's avatar
Stevenn Volant committed
199
             ),
stevenn's avatar
stevenn committed
200
201
202
              column(12,uiOutput("TabBoxData"))

              
Stevenn Volant's avatar
Stevenn Volant committed
203
          
stevenn's avatar
stevenn committed
204
205
    ),
    
stevenn's avatar
stevenn committed
206
207
208
  #### Statistical analysis

    tabItem(tabName = "RunDiff",
stevenn's avatar
stevenn committed
209
210
211
            fluidRow(
              column(width=3,infoBoxOutput("RowTarget",width=NULL)),
              column(width=3,infoBoxOutput("InfoTaxo",width=NULL)),
212
213
              column(width=3,infoBoxOutput("InfoDESeq",width=NULL)),
              column(width=3,conditionalPanel(condition="input.RunDESeq>=1",infoBoxOutput("InfoContrast",width=NULL)))
Stevenn Volant's avatar
Stevenn Volant committed
214
            ),            
stevenn's avatar
stevenn committed
215
            fluidRow(
stevenn's avatar
stevenn committed
216
217
218
              column(width=5,
                box(title="Experimental design",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
                  fluidRow(
stevenn's avatar
stevenn committed
219
220
                    column(width=6,fileInput('fileTarget', h6(strong('Select your target file')),width="100%")),
                    column(width=6,uiOutput("SelectTaxo"))
stevenn's avatar
stevenn committed
221
222
223
224
                  ),
                  fluidRow( 
                    column(width=6,uiOutput("SelectInterestVar")),
                    column(width=6,uiOutput("SelectInteraction2")),
225
                    column(width=6,uiOutput("RunButton"))
stevenn's avatar
stevenn committed
226
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
227
228
229
                ),
                uiOutput("BoxTarget"),
                uiOutput("BoxCountsMerge")
stevenn's avatar
stevenn committed
230
              ),
stevenn's avatar
stevenn committed
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
       
              column(width=7,
                box(title="Options",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
                  fluidRow(
                    column(width=3,
                      radioButtons("TransType",h6(strong("Type of transformation")),choices = c("VST"="VST","rlog"="rlog"))
                    ), 
                    column(width=3,
                      radioButtons("IndFiltering",h6(strong("Independent filtering")),choices = c("True"=TRUE,"False"=FALSE))
                    ),
                    column(width=3,
                      radioButtons("AdjMeth",h6(strong("p-value adjustement")),choices = c("BH"="BH","BY"="BY"))
                    ),
                    column(width=3,
                      textInput("AlphaVal",h6(strong("Level of significance")),value=0.05)
                    )
                  ),
                  fluidRow(
                    column(width=3,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
250
                           radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='Auto',"No cut-off"=Inf,"Value"="val")),
stevenn's avatar
stevenn committed
251
252
253
254
255
256
257
258
259
                           conditionalPanel(condition="input.CooksCutOff=='val'",textInput("CutOffVal",h6("Cut-off:"),value=0))
                    ),
                    
                    column(width=3,
                      radioButtons("locfunc",h6(strong("Local function")),choices = c("Median"="median","Shorth"="shorth"))
                    ),  
                    column(width=3,
                      radioButtons("fitType",h6(strong("Relationship")),choices = c("Parametric"="parametric","Local"="local"))
                    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
260
261
262
263
264
                    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)
                      )
                    ),
stevenn's avatar
stevenn committed
265
266
                    column(width=3,uiOutput("RefSelect"))
                  )
stevenn's avatar
stevenn committed
267
                ),
268
269
270
271
272
273
274
275
276
                fluidRow(
                column(width=8,
                       uiOutput("contrastBox"),
                       uiOutput("contrastBoxAdvanced")
                       ),
                column(width=4,
                       uiOutput("contrastDefined")
                )  
                ) 
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
277
              )
stevenn's avatar
stevenn committed
278
279
            )
            
stevenn's avatar
stevenn committed
280
    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
281
    tabItem(tabName = "DiagPlotTab",
stevenn's avatar
stevenn committed
282
            fluidRow(
stevenn's avatar
stevenn committed
283
              column(width=9,
Stevenn Volant's avatar
Stevenn Volant committed
284
285
286
                     
                plotOutput("PlotDiag",height="100%"),
                br(),
287
                conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
stevenn's avatar
stevenn committed
288
289
290
                  box(title = "Size factors",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                    dataTableOutput("SizeFactTable")
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
291
292
293
294
                ),
                  
                conditionalPanel(condition="input.DiagPlot=='pcaPlot'",
                                 box(title = "Eigen values",  width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
Stevenn Volant's avatar
Stevenn Volant committed
295
                                    plotOutput("PlotEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
296
297
298
299
                                 )
                ),
                conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
                                 box(title = "Eigen values",  width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
Stevenn Volant's avatar
Stevenn Volant committed
300
                                     plotOutput("PlotpcoaEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
301
                                 )
stevenn's avatar
stevenn committed
302
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
303
                
stevenn's avatar
stevenn committed
304
305
              ),
              column(width=3,
306
307
308
309
310
311
                box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
                  selectInput("DiagPlot","",c("Total barplot"="barplotTot","Nul barplot"="barplotNul",
                                              "Maj. taxonomy"="MajTax", "Density"="densityPlot", 
                                              "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","Clustering" = "clustPlot",
                                              "SERE" = "SERE"))
                    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
312
                box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
313
                    
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
314
315
316
                    conditionalPanel(condition="input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntDiag")),
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot'",
                                     h5(strong("Select the modalities")),
Stevenn Volant's avatar
Stevenn Volant committed
317
318
319
320
321
322
                                     uiOutput("ModMat")
                    ),
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='SERE' || input.DiagPlot=='clustPlot' ",
                      selectInput("DistClust","Distance",c("euclidean", "SERE"="sere", "canberra", "bray", "kulczynski", "jaccard", 
                                                         "gower", "altGower", "morisita", "horn","mountford","raup","binomial",
                                                         "chao","cao","mahalanobis"),selected="jaccard")
323
                    )
Stevenn Volant's avatar
Stevenn Volant committed
324
                    
stevenn's avatar
stevenn committed
325
326
327
328
329
330
331
#                 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)) 
               ),
                box(
                  title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
332
333
334
335
#                     conditionalPanel(condition="input.DiagPlot=='Sfactors'",
#                                      h6(strong("Layout")),
#                                      numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
#                     ),
Stevenn Volant's avatar
Stevenn Volant committed
336
337
                  sliderInput("heightDiag", "Height",min=100,max=1500,value = 500,step =10),

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
338
339
340
341
342
343
344
345
346
347
348
349
                  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)
                                   
                  ),
Stevenn Volant's avatar
Stevenn Volant committed
350
351
352
353
354
355
356
357
358
359
360
                  conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
                    checkboxInput("addLabelSFact","Add label",FALSE)
                  ),

                  fluidRow(
                    column(width=12, p(strong("Size"))),
                    column(width=6,sliderInput("cexTitleDiag", h6("Axis"),min=0,max=5,value = 1,step =0.1)),
                    conditionalPanel(condition="input.DiagPlot=='SfactorsVStot' || input.DiagPlot=='pcaPlot'",column(width=6,sliderInput("cexLabelDiag", h6("Points"),min=0,max=5,value = 1,step =0.1)))
                    
                  )

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
361
362
#                   sliderInput("widthDiag", "width",min=100,max=1500,value = 1000,step =10)
                 
stevenn's avatar
stevenn committed
363

stevenn's avatar
stevenn committed
364
365
366
367
368
369
370
371
372
373
374
375
376
377
              ),
              box(title = "Export",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                  selectInput("Exp_format",h5(strong("Export format")),c("png"="png","pdf"="pdf","eps"="eps","svg"="svg"), multiple = FALSE),
                  fluidRow(
                  column(width=6,numericInput("heightDiagExport", "Height (in px)",min=100,max=NA,value = 500,step =1)),
                  column(width=6,numericInput("widthDiagExport", "Width (in px)",min=100,max=NA,value = 500,step =1))
                  ),
                  downloadButton("exportdiag", "Export")
                  
#                   downloadButton("exportPDFdiag", "Download pdf"),
#                   downloadButton("exportPNGdiag", "Download png"),
#                   downloadButton("exportEPSdiag", "Download eps"),
#                   downloadButton("exportSVGdiag", "Download svg"),
                  
stevenn's avatar
stevenn committed
378
379
380
              )
            )
        )
stevenn's avatar
stevenn committed
381
382
383
    ),
    tabItem(tabName = "TableDiff",
            fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
384
385
386
387
388
              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")
389
390
391
392
393
                     ),
                     box(title = "Export",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                         fluidRow(column(width=12,selectInput("WhichExportTable", "Select the table to export",c("Complete"="Complete","Up"="Up","Down"="Down")))),
                         uiOutput("ExportTableButton")   
                     )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
394
395
            )
            )
stevenn's avatar
stevenn committed
396
397
398
399
    ),
  
  #### Data Viz
  
400
  tabItem(tabName = "Visu",
stevenn's avatar
stevenn committed
401
          fluidRow(
402
403
404
            column(width=9,
                  uiOutput("plotVisu")
            ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
405
406

            column(width=3,
407
408
409
410
411
412
413
414
415
416
417
418
419
              box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
                  selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "Barplot")
              ),
              
              
              
              ########################################################################
              ###
              ###               Options Visualization
              ###
              ########################################################################
              
              
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
420
              box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
                  
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction'",
                                    uiOutput("VarIntVisu")
                  ),
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity'",
                                   radioButtons("SelectSpecifTaxo","Select the features",c("Most abundant"="Most","All"="All", "Differential features" = "Diff"))
                  ),
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.SelectSpecifTaxo=='Diff'",
                                   selectizeInput("ContrastList_table_Visu","",choices = "", multiple = FALSE)
                  ),
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity'",
                                   uiOutput("TaxoToPlotVisu")
                  ),

                  
                  
                ##################
                ## BARPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Barplot'",
                                 selectizeInput(inputId = "CountsOrProp",label = h6(strong("Type of data")),choices = c("Proportions" = "prop", "Counts" = "counts"),selected = "prop")
                ),
                
                
                ##################
                ## HEATMAP
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Heatmap'",
                                 selectizeInput(inputId = "HeatMapType",label = h6(strong("Type of data")),choices = c("Counts" = "Counts", "Log2FC" = "Log2FC"),selected = "Counts")                                 
                ),
                conditionalPanel(condition="input.PlotVisuSelect=='Heatmap' && input.HeatMapType=='Log2FC'",
                                 selectizeInput("ContrastList_table_FC",h6(strong("Contrasts (Min = 2)")),choices = "", multiple = TRUE)
                ),
                conditionalPanel(condition="input.PlotVisuSelect=='Heatmap'",
                                 selectizeInput(inputId = "scaleHeatmap",label = h6(strong("Scale:")),choices = c("None" = "none", "Rows" = "row", "Column" = "col"),selected = "none")
                                 
                ),
                
                ##################
                ## BOXPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Boxplot'",
                                 selectizeInput("typeDataBox",h6(strong("Type of data")),c("Log2"="Log2","Relative"="Relative"))
                ),
                
                ##################
                ## DIVERSITY
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
                                 selectizeInput("WhichDiv",h6(strong("Diversity")),c('Alpha','Beta','Gamma'),selected  = c('Alpha','Beta','Gamma'),multiple=TRUE),
                                 checkboxInput("AddBoxplotDiv","AddBoxplot",value=FALSE)
                ),
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity' && input.AddBoxplotDiv",
                                 uiOutput("SelectVarBoxDiv")
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
476
              ),
477
478
479
480
481
482
483
484
485
              
              
              ########################################################################
              ###
              ###               Appearance Visualization
              ###
              ########################################################################
              
              
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
486
              box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
487
                sliderInput("heightVisu", h6(strong("Height")),min=100,max=4000,value = 800),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
488

Stevenn Volant's avatar
Stevenn Volant committed
489
490

                
491
492
493
494
                ##################
                ## BOXPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Boxplot'",
Stevenn Volant's avatar
Stevenn Volant committed
495
                                 radioButtons("ScaleBoxplot","Scales",c("Fixed"="fixed","Free"="free"),inline=TRUE),
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
                                 checkboxInput("CheckAddPointsBox","Add points",value=TRUE)
                ),
                
                ##################
                ## DIVERSITY
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
                                 sliderInput("sizePointGlobal", h6(strong("Points size")),min=0.5,max=10,value =3,step=0.5),
                                 checkboxInput("SplitVisuGlobal","Split diversity",value=FALSE)
                ),
                
                ##################
                ## 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"))
                ),
                conditionalPanel(condition="input.PlotVisuSelect=='Heatmap'",
                                 fluidRow(
                                   column(width=12,h6(strong("Labels options"))),
                                   column(width=6,sliderInput("LabelSizeHeatmap", h6("Size"),min=0.1,max=2,value = 0.7,step = 0.1)),
                                   column(width=6,sliderInput("LabelOrientHeatmap", h6("Orientation"),min=0,max=90,value = 0,step = 5)),
                                   column(width=6,sliderInput("LabelColOffsetHeatmap", h6("Column offset"),min=0,max=4,value = 0,step = 0.5)),
                                   column(width=6,sliderInput("LabelRowOffsetHeatmap", h6("Row offset"),min=0,max=4,value = 0,step = 0.5)),
                                   
                                   column(width=12,h6(strong("Margins options"))),
                                   column(width=6,sliderInput("rightMargin", h6("Right"),min=0,max=20,value = 6,step = 1)),
                                   column(width=6,sliderInput("lowerMargin", h6("Lower"),min=0,max=20,value = 6,step = 1))
                                 )
                ),              
                
                ##################
                ## ALL
                ##################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
530

531
532
533
534
                conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction'",
                                 radioButtons(inputId = "SensPlotVisu",label = h6(strong("Orientation")),choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical",inline = TRUE)
                )
                
Stevenn Volant's avatar
Stevenn Volant committed
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
              ),
              box(title = "Export",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                  ##################
                  ## BARPLOT
                  ##################
                  conditionalPanel(condition="input.PlotVisuSelect=='Barplot'",
                                   radioButtons("positionBarPlot","Position",c("Grouped"="fill","Stacked"="dodge"),inline=TRUE)
                  ),
                  
                  selectInput("Exp_format_Visu",h5(strong("Export format")),c("png"="png","pdf"="pdf","eps"="eps","svg"="svg"), multiple = FALSE),
                  fluidRow(
                    column(width=6,numericInput("heightVisuExport", "Height (in px)",min=100,max=NA,value = 500,step =1)),
                    column(width=6,numericInput("widthVisuExport", "Width (in px)",min=100,max=NA,value = 500,step =1))
                  ),
                  downloadButton("exportVisu", "Export")
                  
551
              )
Stevenn Volant's avatar
Stevenn Volant committed
552
              
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
553
554
555
            )
          )
  ),
556
  
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
557
558
559



stevenn's avatar
stevenn committed
560
561
  #### Krona plot
  tabItem(tabName = "Krona",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
562
563
564
565
 
         fluidRow(
            column(width=3,tableOutput("krona") )
 #includeHTML("file:///home/aghozlan/workspace/META16S_App/www/text.krona.html")
stevenn's avatar
stevenn committed
566
567
          )  
  )       
stevenn's avatar
stevenn committed
568
              
stevenn's avatar
stevenn committed
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
#              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))
#                        
#                      )
#                    
#               )
#               
#               
#               
#             )
             )
     
stevenn's avatar
stevenn committed
825
826
827
    
    
  )
stevenn's avatar
stevenn committed
828

stevenn's avatar
stevenn committed
829
830
831
832
833
834
835
836
837

# Put them together into a dashboardPage
dashboardPage(skin="blue",
  dashboardHeader(title = "Meta16S"),
  sidebar,
  body
)