ui.R 35.5 KB
Newer Older
Stevenn Volant's avatar
Stevenn Volant committed
1
2
3
4
if(!require(shinydashboard)){
  install.packages('shinydashboard')
  library(shinydashboard)
}
svolant's avatar
svolant committed
5
library(shinyjs)
stevenn's avatar
stevenn committed
6
7
8
9
if (!require(psych)) {
  install.packages('psych')
  library(psych)
}
Stevenn Volant's avatar
Stevenn Volant committed
10

stevenn's avatar
stevenn committed
11
12
13
14
if (!require(ggplot2)) {
  install.packages('ggplot2')
  library(ggplot2)
}
Stevenn Volant's avatar
Stevenn Volant committed
15

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

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

stevenn's avatar
stevenn committed
26
27
28
29
if (!require(circlize)) {
  install.packages('circlize')
  library(circlize)
}
Stevenn Volant's avatar
Stevenn Volant committed
30

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

stevenn's avatar
stevenn committed
36
37
38
39
if (!require(DT)) {
  install.packages('DT')
  library(DT)
}
Stevenn Volant's avatar
Stevenn Volant committed
40

stevenn's avatar
stevenn committed
41
42
43
44
if (!require(RColorBrewer)) {
  install.packages('RColorBrewer')
  library(RColorBrewer)
}
Stevenn Volant's avatar
Stevenn Volant committed
45

svolant's avatar
svolant committed
46
47
48
49
50
if (!require(scatterD3)) {
  install.packages('scatterD3')
  library(scatterD3)
}

stevenn's avatar
stevenn committed
51
52
53
54
if (!require(gplots)) {
  install.packages('gplots')
  library(gplots)
}
Stevenn Volant's avatar
Stevenn Volant committed
55

stevenn's avatar
stevenn committed
56
57
58
59
60
if (!require(DESeq2)) {
  source("https://bioconductor.org/biocLite.R")
  biocLite("DESeq2")
  library(DESeq2)
}
Stevenn Volant's avatar
Stevenn Volant committed
61

stevenn's avatar
stevenn committed
62
63
64
if (!require(ade4)) {
  install.packages('ade4')
  library(ade4)
Stevenn Volant's avatar
Stevenn Volant committed
65
}
stevenn's avatar
stevenn committed
66

Stevenn Volant's avatar
Stevenn Volant committed
67
if (!require(genefilter)) {
68
69
  source("https://bioconductor.org/biocLite.R")
  biocLite("genefilter")
Stevenn Volant's avatar
Stevenn Volant committed
70
71
72
  library(genefilter)
}

stevenn's avatar
stevenn committed
73
74
75
sidebar <- dashboardSidebar(
  sidebarMenu(
    menuItem("Home", tabName = "Home", icon = icon("home")),
76
    menuItem("Tutorial", tabName = "Tutorial", icon = icon("book")),
stevenn's avatar
stevenn committed
77
    menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
Stevenn Volant's avatar
logo    
Stevenn Volant committed
78
    menuItemOutput("dymMenu"),
Stevenn Volant's avatar
Stevenn Volant committed
79
    img(src = "logo.jpg", height = 49, width = 220,style="position:absolute;bottom:0;margin:0 0 15px 10px;")
stevenn's avatar
stevenn committed
80
81
82
83
84
85
  )
)

body <- dashboardBody(
  tabItems(
    tabItem(tabName = "Home",
86
87
            div(style="width:100% ; max-width: 1200px",
              tabBox(title="Welcome to SHAMAN", id="tabset1", width=NULL,
88
89
                   tabPanel("About", tags$script(type="text/javascript", language="javascript", src="google-analytics.js"),
                            p("SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization,
Stevenn Volant's avatar
Stevenn Volant committed
90
                                       the differential analysis and mutiple visualization.",style = "font-family: 'times'; font-si16pt"),
Stevenn Volant's avatar
Stevenn Volant committed
91
92
                            p("SHAMAN 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/"),
                              ". SHAMAN 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"),".
Stevenn Volant's avatar
Stevenn Volant committed
93
                              Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995].
94
95
                              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/"), ".
                              A presentation about SHAMAN is available", a("here",target="_blank",href="shaman_presentation.pdf"),style = "font-family: 'times'; font-si16pt"),
Stevenn Volant's avatar
Stevenn Volant committed
96
                            p("Hereafter is the global workflow of the SHAMAN application:"),
Stevenn Volant's avatar
Stevenn Volant committed
97
                            div(img(src = "Workflow.png",width = "100%",style="max-width: 600px"),Align="center")
Stevenn Volant's avatar
Stevenn Volant committed
98
                            ),
Stevenn Volant's avatar
Stevenn Volant committed
99
                   tabPanel("Authors", h3("The main contributors to SHAMAN:"),
Stevenn Volant's avatar
Stevenn Volant committed
100
101
102
103
104
105
106
107
                            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:"),
Stevenn Volant's avatar
Stevenn Volant committed
108
                            p(a("Christophe Malabat",href="mailto:christophe.malabat@pasteur.fr"),a(", Julien Tap",href="mailto:julien.tap@danone.com"),a(", Anna Zhukova",href="mailto:anna.zhukova@pasteur.fr"), a(", Rachel Torchet",href="mailto:rachel.torchet@pasteur.fr"))
Stevenn Volant's avatar
logo    
Stevenn Volant committed
109
                          ),
Stevenn Volant's avatar
Stevenn Volant committed
110
                   tabPanel("Citing SHAMAN",p("No papers about SHAMAN have been published yet, but a manuscript is in preparation.",style = "font-family: 'times'; font-si16pt"),
111
112
113
                            p("For now, if you have any comments, questions or suggestions, or want to use SHAMAN please contact authors", a("here", href="mailto:shaman@pasteur.fr"),".", style = "font-family: 'times'; font-si16pt; color:red")
            )))
    ),
Stevenn Volant's avatar
Stevenn Volant committed
114

115
    tabItem(tabName = "Tutorial",
116
117
            div(style="width:100% ; max-width: 1200px",
            tabBox(title="How to use SHAMAN", id="tabset1", width =NULL,
118
119
120
121
122
123
124
125
            tabPanel("Introduction",
            p(" You can test SHAMAN with the dataset from", a("[Tap et al. 2015]",href="http://www.ncbi.nlm.nih.gov/pubmed/26235304"),
              ", which is available", a("here",target="_blank",href="Alimintest.zip"),"."),
            p("The zip archive contains 4 different files :", br(),
              "- the otu count matrix : Alimintest_otu_table.csv,", br(),
              "- the otu annotation table : Alimintest_otu_table.csv,", br(),
              "- the experimental design : Alimintest_target.csv,", br(),
              "- the contrast table : Alimintest_contrasts.csv."),
126
127
            p("Two groups of person follow two  strict diet periods that involve the intake of 40g following 10g of fiber per day, or 10g of fiber after a 40g fiber intake period:"),
            img(src = "tutorial/FigS1.png",width = "100%",style="max-width: 900px"),
128
129
130
            p("The 16S rRNA (V3 - V4 regions) from fece samples was sequenced at time stamp : 2, 3, 4 and 5.", br(),
              "The analysis will consider the different impact of the different fiber intake and the comparison to patient metabolic data.")),
            tabPanel("1-Load 16S data",
131
            p("The first step consists to load the count matrix and the annotation table as follow :"),
132
            p("- Select 'Upload your data'", br(),
133
134
              "- Load the count table :",br(), img(src = "tutorial/tutorial_upload1.png",width = "100%",style="max-width: 900px"),hr(),
              "- Load the annotation table :", br(), img(src = "tutorial/tutorial_upload2.png",width = "100%",style="max-width: 900px"),hr(),
135
              "- When successfully loaded, the tables are accessible as bellow :",br(),
136
              img(src = "tutorial/tutorial_upload3.png",width = "100%",style="max-width: 600px"),img(src = "tutorial/tutorial_upload4.png",width = "100%",style="max-width: 600px"))),
137
            tabPanel("2-Differential analysis",
138
            p("The second step consists to load the experimental design and the contrast table as follow :"),
139
            p("- Select 'Run differential analysis'",br(),
140
141
142
143
144
145
146
              "- Load the target file :",br(),img(src = "tutorial/tutorial_target.png",width = "100%",style="max-width: 800px"),hr(),
              "- Identify the taxonomy level where the analysis will be performed :",br(),img(src = "tutorial/tutorial_target1.png",width = "100%",style="max-width: 800px"),hr(),
              "- Identify the interactions :",br(),img(src = "tutorial/tutorial_target2.png",width = "100%",style="max-width: 800px"),hr(),
              "- Run the analysis :",br(),img(src = "tutorial/tutorial_target3.png",width = "100%",style="max-width: 800px"),hr(),
              "- When successfully loaded, the tables are accessible as bellow :",br(),img(src = "tutorial/tutorial_target4.png",width = "100%",style="max-width: 800px")),hr(),
            p("- Finally, load the contrast file :",br(),img(src = "tutorial/tutorial_contraste.png",width = "100%",style="max-width: 800px"),hr(),
              "- Contrasts can be visualized as follow :",br(),img(src = "tutorial/tutorial_contraste1.png",width = "100%",style="max-width: 400px"))),
147
            tabPanel("3-Diagnostic plots",
148
149
150
151
152
153
154
155
156
            p("'Diagnostic plots' section provides several visualizations to control the analysis",br(),
              "- Total mapped read count",br(),img(src="tutorial/tutorial_total_barplot.png",width = "100%",style="max-width: 900px"),hr(),
              "- Nul barplot count",br(),img(src="tutorial/tutorial_nul_barplot.png",width = "100%",style="max-width: 900px"),hr(),
              "- Maj taxonomy count",br(),img(src="tutorial/tutorial_maj_taxonomy.png",width = "100%",style="max-width: 900px"),hr(),
              "- Density of counts",br(),img(src="tutorial/tutorial_density.png",width = "100%",style="max-width: 900px"),hr(),
              "- Size factors vs total number of reads",br(),img(src="tutorial/tutorial_size_factor.png",width = "100%",style="max-width: 900px"),hr(),
              "- PCA",br(),img(src="tutorial/tutorial_pca.png",width = "100%",style="max-width: 900px"),hr(),
              "- PCOA",br(),img(src="tutorial/tutorial_pcoa.png",width = "100%",style="max-width: 900px"),hr(),
              "- Clustering",br(),img(src="tutorial/tutorial_clustering.png",width = "100%",style="max-width: 900px"))),
157
            tabPanel("4-Differential analysis results",
158
            img(src = "tutorial/tutorial_table.png",width = "100%",style="max-width: 900px")),
159
160
            tabPanel("5-Visualization",
                     p("'Diagnostic plots' section provides several visualization to control the analysis",br(),
161
162
163
164
165
                     "- Barplot",br(),img(src="tutorial/tutorial_barplot.png",width = "100%",style="max-width: 900px"),hr(),
                     "- Heatmap",br(),img(src="tutorial/tutorial_heatmap.png",width = "100%",style="max-width: 900px"),hr(),
                     "- Boxplot",br(),img(src="tutorial/tutorial_boxplot.png",width = "100%",style="max-width: 900px"),hr(),
                     "- Diversity",br(),img(src="tutorial/tutorial_diversity.png",width = "100%",style="max-width: 900px"),hr(),
                     "- Rarefaction",br(),img(src="tutorial/tutorial_rarefaction.png",width = "100%",style="max-width: 900px")))))
166
    ),
Stevenn Volant's avatar
Stevenn Volant committed
167
    
stevenn's avatar
stevenn committed
168
169
170
    tabItem(tabName = "Upload",
            tags$style(type='text/css', ".well { max-width: 20em; }"),
            fluidRow(
Stevenn Volant's avatar
Stevenn Volant committed
171
172
173
174
175
176
177
              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,
178
                  selectInput("FileFormat","",c("Count table & taxonomy"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts")
Stevenn Volant's avatar
Stevenn Volant committed
179
                ),
stevenn's avatar
stevenn committed
180
                conditionalPanel(condition="input.FileFormat=='fileCounts'",
181
                  box(title="Load the count table",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
182
                    fileInput('fileCounts', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
183
                  ),
stevenn's avatar
stevenn committed
184
                  
Stevenn Volant's avatar
Stevenn Volant committed
185
186
187
188
189
190
191
                  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
192
                      fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
193
194
195
196
197
                  )
                  
                ),
                
                conditionalPanel(condition="input.FileFormat=='fileBiom'",
Stevenn Volant's avatar
Stevenn Volant committed
198
                                 box(title="Load the BIOM file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
199
200
201
                                     fileInput('fileBiom', h5(strong('Select your file')),width="100%")
                                 )           
                )
Stevenn Volant's avatar
Stevenn Volant committed
202
             ),
stevenn's avatar
stevenn committed
203
204
205
              column(12,uiOutput("TabBoxData"))

              
Stevenn Volant's avatar
Stevenn Volant committed
206
          
stevenn's avatar
stevenn committed
207
208
    ),
    
stevenn's avatar
stevenn committed
209
210
211
  #### Statistical analysis

    tabItem(tabName = "RunDiff",
stevenn's avatar
stevenn committed
212
213
214
            fluidRow(
              column(width=3,infoBoxOutput("RowTarget",width=NULL)),
              column(width=3,infoBoxOutput("InfoTaxo",width=NULL)),
215
              column(width=3,infoBoxOutput("InfoDESeq",width=NULL)),
216
              column(width=3,infoBoxOutput("InfoContrast",width=NULL))
Stevenn Volant's avatar
Stevenn Volant committed
217
            ),            
stevenn's avatar
stevenn committed
218
            fluidRow(
stevenn's avatar
stevenn committed
219
220
221
              column(width=5,
                box(title="Experimental design",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
                  fluidRow(
stevenn's avatar
stevenn committed
222
223
                    column(width=6,fileInput('fileTarget', h6(strong('Select your target file')),width="100%")),
                    column(width=6,uiOutput("SelectTaxo"))
stevenn's avatar
stevenn committed
224
225
226
227
                  ),
                  fluidRow( 
                    column(width=6,uiOutput("SelectInterestVar")),
                    column(width=6,uiOutput("SelectInteraction2")),
228
                    column(width=6,uiOutput("RunButton"))
stevenn's avatar
stevenn committed
229
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
230
231
232
                ),
                uiOutput("BoxTarget"),
                uiOutput("BoxCountsMerge")
stevenn's avatar
stevenn committed
233
              ),
stevenn's avatar
stevenn committed
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
       
              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
253
                           radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='Auto',"No cut-off"=Inf,"Value"="val")),
stevenn's avatar
stevenn committed
254
255
256
257
258
259
260
261
262
                           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"))
                    ),
263
264
                    column(width=3,checkboxInput("AccountForNA","Compute geometric mean without 0",value=TRUE))
                    # column(width=3,uiOutput("RefSelect"))
stevenn's avatar
stevenn committed
265
                  )
stevenn's avatar
stevenn committed
266
                ),
267
268
                fluidRow(
                column(width=8,
Stevenn Volant's avatar
Stevenn Volant committed
269
#                        uiOutput("contrastBox"),
270
271
272
273
                       uiOutput("contrastBoxAdvanced")
                       ),
                column(width=4,
                       uiOutput("contrastDefined")
274
275
                )
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
276
              )
stevenn's avatar
stevenn committed
277
            )
stevenn's avatar
stevenn committed
278
    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
279
    tabItem(tabName = "DiagPlotTab",
stevenn's avatar
stevenn committed
280
            fluidRow(
stevenn's avatar
stevenn committed
281
              column(width=9,
Stevenn Volant's avatar
Stevenn Volant committed
282
283
284
                     
                plotOutput("PlotDiag",height="100%"),
                br(),
285
                conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
stevenn's avatar
stevenn committed
286
287
288
                  box(title = "Size factors",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                    dataTableOutput("SizeFactTable")
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
289
290
291
292
                ),
                  
                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
293
                                    plotOutput("PlotEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
294
295
296
297
                                 )
                ),
                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
298
                                     plotOutput("PlotpcoaEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
299
                                 )
stevenn's avatar
stevenn committed
300
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
301
                
stevenn's avatar
stevenn committed
302
303
              ),
              column(width=3,
304
305
                box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
                  selectInput("DiagPlot","",c("Total barplot"="barplotTot","Nul barplot"="barplotNul",
306
                                              "Maj. taxonomy"="MajTax", "Density"="densityPlot", "Dispersion" = "DispPlot",
307
                                              "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","Clustering" = "clustPlot"))
308
                    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
309
                box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
310
311
312
                    conditionalPanel(condition="input.DiagPlot!='clustPlot' && input.DiagPlot!='pcaPlot' && input.DiagPlot!='SfactorsVStot' && input.DiagPlot!='DispPlot'",
                                     radioButtons("CountsType","Counts:",c("Normalized"="norm","Raw"="raw"),inline = TRUE)
                                     ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
313
                    conditionalPanel(condition="input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntDiag")),
314
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='pcaPlot'",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
315
                                     h5(strong("Select the modalities")),
Stevenn Volant's avatar
Stevenn Volant committed
316
                                     uiOutput("ModMat")
317
                                    ),
Stevenn Volant's avatar
Stevenn Volant committed
318
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='SERE' || input.DiagPlot=='clustPlot' ",
319
320
321
322
                                      selectInput("DistClust","Distance",c("euclidean", "SERE"="sere", "canberra", "bray", "kulczynski", "jaccard", 
                                                  "gower", "altGower", "morisita", "horn","mountford","raup","binomial",
                                                  "chao","cao","mahalanobis"),selected="jaccard")
                                    )
Stevenn Volant's avatar
Stevenn Volant committed
323
                    
stevenn's avatar
stevenn committed
324
325
326
327
328
329
330
#                 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,
331
332
333
334
#                     conditionalPanel(condition="input.DiagPlot=='Sfactors'",
#                                      h6(strong("Layout")),
#                                      numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
#                     ),
Stevenn Volant's avatar
Stevenn Volant committed
335
336
                  sliderInput("heightDiag", "Height",min=100,max=1500,value = 500,step =10),

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
337
338
339
340
341
342
343
344
345
346
347
348
                  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
349
350
351
352
353
354
355
                  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)),
356
                    conditionalPanel(condition="input.DiagPlot=='SfactorsVStot' || input.DiagPlot=='pcaPlot' || input.DiagPlot=='pcoaPlot'",column(width=6,sliderInput("cexLabelDiag", h6("Points"),min=0,max=5,value = 1,step =0.1)))
Stevenn Volant's avatar
Stevenn Volant committed
357
358
359
                    
                  )

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
360
361
#                   sliderInput("widthDiag", "width",min=100,max=1500,value = 1000,step =10)
                 
stevenn's avatar
stevenn committed
362

stevenn's avatar
stevenn committed
363
364
365
366
367
368
369
370
371
372
373
374
375
376
              ),
              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
377
378
379
              )
            )
        )
stevenn's avatar
stevenn committed
380
381
382
    ),
    tabItem(tabName = "TableDiff",
            fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
383
384
385
386
387
              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")
388
389
390
391
392
                     ),
                     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
393
            )
Stevenn Volant's avatar
Stevenn Volant committed
394
            ) 
stevenn's avatar
stevenn committed
395
396
397
398
    ),
  
  #### Data Viz
  
399
  tabItem(tabName = "Visu",
stevenn's avatar
stevenn committed
400
          fluidRow(
401
            column(width=9,
svolant's avatar
svolant committed
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
                   uiOutput("plotVisu"),
                   conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot' && !input.AddRegScatter",
                                    useShinyjs(),
                                    br(),
                                    p(actionButton("scatterD3-reset-zoom", HTML("<span class='glyphicon glyphicon-search' aria-hidden='true'></span> Reset Zoom")),Align="right")
                                    ), 
                   conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot' && input.AddRegScatter", 
                                    column(width=6,
                                           br(),
                                           box(title = "Regression coefficients",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                                                dataTableOutput("lmRegScatter")
                                           )
                                    ),
                                    column(width=6,br(),htmlOutput("lmEquation"))
                   )
                                    
                   ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
419
420

            column(width=3,
421
              box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
svolant's avatar
svolant committed
422
                  selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "Scatterplot")
423
              ),
424
425


426
427
428
429
430
              ########################################################################
              ###
              ###               Options Visualization
              ###
              ########################################################################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
431
              box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
svolant's avatar
svolant committed
432
433
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Scatterplot' ",
                                   uiOutput("VarIntVisu"),
434
435
                                   h5(strong("Select the modalities")),
                                   uiOutput("ModVisu")
436
                  ),
svolant's avatar
svolant committed
437
438
439
440
441
                  conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot' ",
                                   uiOutput("VarIntVisuScatter"),
                                   checkboxInput("AddRegScatter","Add regression line",FALSE)
                  ),                 
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot'",
svolant's avatar
svolant committed
442
                                   radioButtons("SelectSpecifTaxo","Select the features",c("Most abundant"="Most","All"="All", "Differential features" = "Diff", "Non differential features" = "NoDiff"))
443
                  ),
svolant's avatar
svolant committed
444
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot' && (input.SelectSpecifTaxo=='Diff' || input.SelectSpecifTaxo=='NoDiff') ",
445
446
                                   selectizeInput("ContrastList_table_Visu","",choices = "", multiple = FALSE)
                  ),
svolant's avatar
svolant committed
447
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot'",
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
                                   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
490
              ),
491
492


493
494
495
496
497
              ########################################################################
              ###
              ###               Appearance Visualization
              ###
              ########################################################################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
498
              box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
499
                sliderInput("heightVisu", h6(strong("Height")),min=100,max=4000,value = 800),
500
501
502
503
                ##################
                ## BOXPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Boxplot'",
504
                                 uiOutput("ColBoxplot"),
Stevenn Volant's avatar
Stevenn Volant committed
505
                                 radioButtons("ScaleBoxplot","Scales",c("Fixed"="fixed","Free"="free"),inline=TRUE),
506
507
508
509
510
511
512
513
514
515
516
517
518
                                 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'",
Stevenn Volant's avatar
Stevenn Volant committed
519
                                 selectInput("colors", label=h6(strong("Gradient of colors")),choices = c("green-blue", "blue-white-red", "purple-white-orange", "red-yellow-green"),selected = "blue-white-red")
520
521
522
523
524
525
526
527
528
529
530
531
                ),
                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))
                                 )
532
                ),
svolant's avatar
svolant committed
533
534
535
536
537
538
539
540
541
542
                
                ##################
                ## Scatterplot
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot'",
                                 fluidRow(
                                   column(width=12,sliderInput("SizeLabelScatter", h6("Label size"),min=0,max=50,value = 10,step = 1))
                                  )
                ),
                
543
544
545
546
547
548
                ##################
                ## ALL
                ##################
                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
549
550
551
552
553
554
555
556
557
558
559
560
561
562
              ),
              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")
563
              )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
564
565
566
567
            )
          )
  ),

stevenn's avatar
stevenn committed
568
569
  #### Krona plot
  tabItem(tabName = "Krona",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
570
         fluidRow(
Stevenn Volant's avatar
Stevenn Volant committed
571
572
573
574
575
576
577
578
579
580
581
582
            column(width=3,
                   p(strong("Krona plot")),
                   img(src="Krona.png",height = 200, width = 220),
                   a(href = "test_krona.html",target="_blank", "Click Here!")
#                    tableOutput("krona") 

),
            column(width=3,
            p(strong("Tree abundance")),
            img(src="Tree.png",height = 200, width = 220),
            a(href = "http://genopole.pasteur.fr/SynTView/flash/TreeAbundance",target="_blank", "Click Here!")
            )
583
        )
Stevenn Volant's avatar
Stevenn Volant committed
584
 #includeHTML("file:///home/aghozlan/workspace/SHAMAN_App/www/text.krona.html")
stevenn's avatar
stevenn committed
585
  )
586
587
588
 )
)
  ## GOOGLE ANALYTIC
589
 #tags$head(includeScript("google-analytics.js"))
Stevenn Volant's avatar
logo    
Stevenn Volant committed
590
591
592
593
  ## Logo SHAMAN
  dbHeader <- dashboardHeader(title = "SHAMAN")
  dbHeader$children[[2]]$children <-  tags$a(tags$img(src='akuaku.png',height='40',width='50',style="margin:5px 0 5px 0;",align='left'), tags$h3("SHAMAN",style="font-family:Purisa; margin:15px 25px 5px 0;color:white;"))
  
stevenn's avatar
stevenn committed
594
# Put them together into a dashboardPage
Stevenn Volant's avatar
logo    
Stevenn Volant committed
595
596
597
598
599
  dashboardPage(skin="blue",
    dbHeader,
    sidebar,
    body
  )
stevenn's avatar
stevenn committed
600
601