ui.R 37.1 KB
Newer Older
stevenn's avatar
stevenn committed
1
2
3
4

library(shinydashboard)
library(DT)
library(biom)
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
5
6
7
8
9
10
11
12
library(DESeq2)
library(rNVD3)
library(RColorBrewer)
library(gplots)
library(ggdendro)
library(dendextend)
library(circlize)
library(ade4)
stevenn's avatar
stevenn committed
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37

sidebar <- dashboardSidebar(
  sidebarMenu(
    menuItem("Home", tabName = "Home", icon = icon("home")),
    menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
    menuItemOutput("dymMenu")
  )
)

body <- dashboardBody(
  tabItems(
    tabItem(tabName = "Home",
            h2("Bienvenue !")
    ),
    tabItem(tabName = "Upload",
            tags$style(type='text/css', ".well { max-width: 20em; }"),
            # Tags:
            tags$head(
              tags$style(type="text/css", "select[multiple] { width: 100%; height:10em}"),
              tags$style(type="text/css", "select { width: 100%}"),
              tags$style(type="text/css", "input { width: 19em; max-width:100%}")
            ),
            fluidRow(
              column(12,
                  h3(strong("Instructions")),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
38
39
40
41
                   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")
stevenn's avatar
stevenn committed
42
              ),
stevenn's avatar
stevenn committed
43
44
              br(),
              
stevenn's avatar
stevenn committed
45
46
              column(3,
                box(title="Select your file format",width = NULL, status = "success", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
47
                  selectInput("FileFormat","",c("Counts table & taxonomy"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts")
stevenn's avatar
stevenn committed
48
                )
stevenn's avatar
stevenn committed
49
                #uiOutput("LoadButton")
stevenn's avatar
stevenn committed
50
51
52
53
              ),
              column(9,
                conditionalPanel(condition="input.FileFormat=='fileCounts'",
                  box(title="Load the counts table",width = 4, status = "primary", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
54
                    fileInput('fileCounts', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
55
                  ),
stevenn's avatar
stevenn committed
56
                  
stevenn's avatar
stevenn committed
57
                  box(title="Load the taxonomy file",width = 4, status = "primary", solidHeader = TRUE,collapsible = FALSE,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
58
                      radioButtons("TypeTaxo",h6(strong("Format:")),c("Table"="Table","RDP"="RDP")),
stevenn's avatar
stevenn committed
59
                      fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
60
61
62
63
64
65
66
67
68
69
70
                  )
                  
                ),
                
                conditionalPanel(condition="input.FileFormat=='fileBiom'",
                                 box(title="Load the BIOM file",width = 4, status = "primary", solidHeader = TRUE,collapsible = FALSE,
                                     fileInput('fileBiom', h5(strong('Select your file')),width="100%")
                                 )           
                )
                
              ),
stevenn's avatar
stevenn committed
71
72
73
74
              column(12,uiOutput("TabBoxData"))

              
          )
stevenn's avatar
stevenn committed
75
76
    ),
    
stevenn's avatar
stevenn committed
77
78
79
80
81
82
83
84
    
    
    
    
    
  #### Statistical analysis

    tabItem(tabName = "RunDiff",
stevenn's avatar
stevenn committed
85
86
87
88
89
90
            fluidRow(
              column(width=3,infoBoxOutput("RowTarget",width=NULL)),
              column(width=3,infoBoxOutput("InfoContrast",width=NULL)),
              column(width=3,infoBoxOutput("InfoTaxo",width=NULL)),
              column(width=3,infoBoxOutput("InfoDESeq",width=NULL))
            ),
stevenn's avatar
stevenn committed
91
            fluidRow(
stevenn's avatar
stevenn committed
92
93
94
              column(width=5,
                box(title="Experimental design",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
                  fluidRow(
stevenn's avatar
stevenn committed
95
96
                    column(width=6,fileInput('fileTarget', h6(strong('Select your target file')),width="100%")),
                    column(width=6,uiOutput("SelectTaxo"))
stevenn's avatar
stevenn committed
97
98
99
100
101
102
                  ),
                  fluidRow( 
                    column(width=6,uiOutput("SelectInterestVar")),
                    column(width=6,uiOutput("SelectInteraction2")),
                    column(width=6,actionButton("RunDESeq",strong("Run analysis"),icon = icon("caret-right")))
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
103
104
105
                ),
                uiOutput("BoxTarget"),
                uiOutput("BoxCountsMerge")
stevenn's avatar
stevenn committed
106
              ),
stevenn's avatar
stevenn committed
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
       
              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
126
                           radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='Auto',"No cut-off"=Inf,"Value"="val")),
stevenn's avatar
stevenn committed
127
128
129
130
131
132
133
134
135
                           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
136
137
138
139
140
                    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
141
142
                    column(width=3,uiOutput("RefSelect"))
                  )
stevenn's avatar
stevenn committed
143
                ),
stevenn's avatar
stevenn committed
144
145
146
                box(title="Contrasts",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
                    column(width=3,uiOutput("contrastMat")),
                    column(width=3,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
147
148
                           textInput("ContrastName","Contrast name","Name..."),
                           actionButton("AddContrast","Add contrast",icon = icon("plus"))
stevenn's avatar
stevenn committed
149
150
                    ),
                    column(width=3,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
151
152
                           selectInput("ContrastList","Contrasts","",multiple=TRUE,size=2,selectize=FALSE),
                           actionButton("RemoveContrast","Remove",icon = icon("remove"))
stevenn's avatar
stevenn committed
153
154
                    ),
                    column(width=3,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
155
156
                           h5(strong("Selected contrast:")),
                           htmlOutput("ContrastOverview")
stevenn's avatar
stevenn committed
157
                    ) 
stevenn's avatar
stevenn committed
158
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
159
160
161
                
                
              )
stevenn's avatar
stevenn committed
162
163
            )
            
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
164
165
166
167
168
169
#             fluidRow(
#               column(width=12,
# 
#               )  
#             )
            
stevenn's avatar
stevenn committed
170
    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
171
    tabItem(tabName = "DiagPlotTab",
stevenn's avatar
stevenn committed
172
            fluidRow(
stevenn's avatar
stevenn committed
173
174
              column(width=9,
                box(title = "Plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
175
                  plotOutput("PlotDiag")
stevenn's avatar
stevenn committed
176
177
178
179
180
                ),
                conditionalPanel(condition="input.DiagPlot=='Sfactors'",
                  box(title = "Size factors",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                    dataTableOutput("SizeFactTable")
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
181
182
183
184
185
186
187
188
189
190
191
                ),
                  
                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")
                                 )
stevenn's avatar
stevenn committed
192
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
193
                
stevenn's avatar
stevenn committed
194
195
              ),
              column(width=3,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
                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")
stevenn's avatar
stevenn committed
211
212
213
214
215
216
217
218
219
220
#                 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,
                    conditionalPanel(condition="input.DiagPlot=='Sfactors'",
                                     h6(strong("Layout")),
                                     numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
                    ),
                  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)
                 
stevenn's avatar
stevenn committed
238
239
240
241

              )
            )
        )
stevenn's avatar
stevenn committed
242
243
244
    ),
    tabItem(tabName = "TableDiff",
            fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
245
246
247
248
249
250
251
252
              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")
                      )
            )
            )
stevenn's avatar
stevenn committed
253
254
255
256
    ),
  
  #### Data Viz
  
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
257
  tabItem(tabName = "BarplotVisu",
stevenn's avatar
stevenn committed
258
          fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
            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)
              )
            )
          )
          
stevenn's avatar
stevenn committed
307
  ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
308

stevenn's avatar
stevenn committed
309
  
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
  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)
                       
                   )
            )
          )
          
  ),

stevenn's avatar
stevenn committed
367
  
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
  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)
# #                        
#                    )
#             )
          )
          
  ),

stevenn's avatar
stevenn committed
399
400
401
402
403
404
  #### Krona plot
  tabItem(tabName = "Krona",
          fluidRow(
            column(width=3,p("Krona plot"))      
          )  
  )       
stevenn's avatar
stevenn committed
405
              
stevenn's avatar
stevenn committed
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
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
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
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
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
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
#              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
662
663
664
    
    
  )
stevenn's avatar
stevenn committed
665

stevenn's avatar
stevenn committed
666
667
668
669
670
671
672
673
674

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