ui.R 48.4 KB
Newer Older
svolant's avatar
svolant committed
1
2
source("css/owncss.R")
source("Rfunctions/Data_Management.R")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
3
4
5
6
7
8
9
10
11
12
13
14
if(!require(shinydashboard)){
  installed.packages("shinydashboard")
  library(shinydashboard)  
}
if(!require(shinythemes)){
  install.packages("shinythemes")
  library(shinythemes)
}
if(!require(shinyjs)){
  install.packages("shinyjs")
  library(shinyjs)  
}
svolant's avatar
svolant committed
15

svolant's avatar
svolant committed
16
function(request) {
stevenn's avatar
stevenn committed
17
sidebar <- dashboardSidebar(
svolant's avatar
svolant committed
18
19
  useShinyjs(),
  inlineCSS(appCSS),
20
21
22
  tags$head(
    tags$script(src = "custom.js")
  ),
svolant's avatar
svolant committed
23
24
25
26
  div(id = "loading-content-bar",
      p()),
  div(
    id = "app-content-bar",
stevenn's avatar
stevenn committed
27
28
  sidebarMenu(
    menuItem("Home", tabName = "Home", icon = icon("home")),
29
    menuItem("Tutorial", tabName = "Tutorial", icon = icon("book")),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
30
    menuItem("Download/Install (beta)", tabName = "Download", icon = icon("download")),
stevenn's avatar
stevenn committed
31
    menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
svolant's avatar
svolant committed
32
    # bookmarkButton(),
Stevenn Volant's avatar
logo    
Stevenn Volant committed
33
    menuItemOutput("dymMenu"),
Stevenn Volant's avatar
Stevenn Volant committed
34
    img(src = "logo.jpg", height = 49, width = 220,style="position:absolute;bottom:0;margin:0 0 15px 10px;")
stevenn's avatar
stevenn committed
35
  )
svolant's avatar
svolant committed
36
  )
stevenn's avatar
stevenn committed
37
38
39
)

body <- dashboardBody(
svolant's avatar
svolant committed
40
41
42
43
44
45
46
47
48
49
50
51
  tags$style(type="text/css", Errorcss),
  
  useShinyjs(),
  inlineCSS(appCSS),
  div(
    id = "loading-content",
    br(),
    br(),
    br(),
    h2("Please wait while SHAMAN is loading...")),
  div(
    id = "app-content-bar",
stevenn's avatar
stevenn committed
52
53
  tabItems(
    tabItem(tabName = "Home",
svolant's avatar
svolant committed
54
55
            fluidRow(
              column(width=9,
56
            div(style="width:100% ; max-width: 1200px",
svolant's avatar
svolant committed
57
                
58
              tabBox(title="Welcome to SHAMAN", id="tabset1", width=NULL,
59
60
                   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
61
                                       the differential analysis and mutiple visualization.",style = "font-family: 'times'; font-si16pt"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
62
63
                            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/"),a("Jonsson2016]",href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/"),
                              ". 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
64
                              Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995].
65
                              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/"), ".
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
66
67
                              A presentation about SHAMAN is available", a("here.",target="_blank",href="shaman_presentation.pdf"), br(),
                              "SHAMAN is compatible with standard formats for metagenomic analysis. We also provide a complete pipeline for OTU picking and annotation named",a("MASQUE", href="https://github.com/aghozlane/masque") ,"used in production at Institut Pasteur.",style = "font-family: 'times'; font-si16pt"),
Stevenn Volant's avatar
Stevenn Volant committed
68
                            p("Hereafter is the global workflow of the SHAMAN application:"),
Stevenn Volant's avatar
Stevenn Volant committed
69
                            div(img(src = "Workflow.png",width = "100%",style="max-width: 600px"),Align="center")
Stevenn Volant's avatar
Stevenn Volant committed
70
                            ),
Stevenn Volant's avatar
Stevenn Volant committed
71
                   tabPanel("Authors", h3("The main contributors to SHAMAN:"),
Stevenn Volant's avatar
Stevenn Volant committed
72
73
74
75
76
77
78
                            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("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:"),
79
                            p(a("Christophe Malabat, ",href="mailto:christophe.malabat@pasteur.fr"), a("Pierre Lechat, ",href="mailto:pierre.lechat@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
80
                          ),
81
82
83
                   tabPanel("Citing SHAMAN",
                   p("No papers about SHAMAN have been published yet, but a manuscript is in preparation.",style = "font-family: 'times'; font-si16pt"),
                   p("Publication using SHAMAN :",style = "font-family: 'times'; font-si18pt; font-style: strong"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
84
                   p(a("A bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection.", href="http://www.ncbi.nlm.nih.gov/pubmed/27140611"), "Quereda JJ, Dussurget O, Nahori MA, Ghozlane A, Volant S, Dillies MA, Regnault B, Kennedy S, Mondot S, Villoing B, Cossart P, Pizarro-Cerda J.; PNAS 2016",style = "font-family: 'times'; font-si16pt"),
85
                   p("If you have any comments, questions or suggestions, or need help to use SHAMAN, please contact authors", a("here", href="mailto:shaman@pasteur.fr"),".", style = "font-family: 'times'; font-si16pt; color:red")
svolant's avatar
svolant committed
86
87
88
89
90
            )))),
              column(width=3,
            box(
              title = "What's new in SHAMAN", width = NULL, status = "primary",
              div(style = 'overflow-y: scroll; max-height: 400px',
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
91
                  addNews("Sep 14th 2016","Download and install SHAMAN","You can install SHAMAN (beta)."),
svolant's avatar
svolant committed
92
93
94
95
96
97
98
99
100
101
                  addNews("Sep 9th 2016","PCA/PCOA","You can select the axes for the PCOA and PCA plots."),
                  addNews("Aug 1st 2016","Biom format","SHAMAN can now support all the Biom format versions."),
                  addNews("Jun 24th 2016","Comparisons plots","The venn diagram and the heatmap of foldchange 
                                                                have been added to compare the results of 2 or more contrasts"),
                  addNews("Jun 17th 2016","Diversity plots","Enhancement of the visualtisation of the diverties. 
                                                              The shanon and inv. shanon have been added")
                  )
            )
              )
              )
102
    ),
Stevenn Volant's avatar
Stevenn Volant committed
103

104
    tabItem(tabName = "Tutorial",
105
106
            div(style="width:100% ; max-width: 1200px",
            tabBox(title="How to use SHAMAN", id="tabset1", width =NULL,
107
108
109
110
111
112
113
114
            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."),
115
116
            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"),
117
118
119
            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",
120
            p("The first step consists to load the count table and the annotation table as follow :"),
121
            p("- Select 'Upload your data'", br(),
122
123
              "- 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(),
124
              "- When successfully loaded, the tables are accessible as bellow :",br(),
125
              img(src = "tutorial/tutorial_upload3.png",width = "100%",style="max-width: 600px"),img(src = "tutorial/tutorial_upload4.png",width = "100%",style="max-width: 600px"))),
126
            tabPanel("2-Differential analysis",
127
            p("The second step consists to load the experimental design and the contrast table as follow :"),
128
            p("- Select 'Run differential analysis'",br(),
129
130
131
132
133
134
135
              "- 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"))),
136
            tabPanel("3-Diagnostic plots",
137
138
139
140
141
142
143
144
145
            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"))),
146
            tabPanel("4-Differential analysis results",
147
            img(src = "tutorial/tutorial_table.png",width = "100%",style="max-width: 900px")),
148
149
            tabPanel("5-Visualization",
                     p("'Diagnostic plots' section provides several visualization to control the analysis",br(),
150
151
152
153
                     "- 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(),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
154
155
                     "- Rarefaction",br(),img(src="tutorial/tutorial_rarefaction.png",width = "100%",style="max-width: 900px"))),
            tabPanel("6-Other datasets available",
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
            p("You can test SHAMAN with two other datasets : "),
            p("- Bacteriocin impact on mice microbiota from ", a("[Quereda et al. 2016]",href="http://www.ncbi.nlm.nih.gov/pubmed/27140611"), ":", a("here",target="_blank",href="listeria.zip"), br(),br(),
              
              "The project is divided into three group :  WT, Delta : Bacteriocin KO, Delta-complemented: Bacteriocin KO + complementation.", br(),
              "Three time points are considered :", br(),
              "- T0 : merged counts from -48H and -24H", br(),
              "- T2 : 6H after listeria infection", br(),
              "- T3 : 24H after listeria infection", br(),
              
              img(src="listeria.png",width = "100%",style="max-width: 500px"),br(),br(),
              
              "Analysis with SHAMAN:", br(),
              "Set variables: condition, time, mice", br(),
              "Set interactions:",
              "1. condition:mice", br(),
              "2. condition:time", br(),hr(),
              "- MOCK communities from ", a("[The NIH HMP Working Group, 2009]",href="http://www.ncbi.nlm.nih.gov/pubmed/19819907"), ":", a("here",target="_blank",href="mock.zip"),br(),
              "Mock communities are composed of 21 species mixed in even or staggered proportions :", br(),br(),
              img(src="mock.png",width = "100%",style="max-width: 600px"),br(),br(),
              "Analysis with SHAMAN: ",br(),
              "Set variables : Community", br(),
              "no interaction"))
              ))
179
    ),
Stevenn Volant's avatar
Stevenn Volant committed
180
    
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
    tabItem(tabName = "Download",
            fluidRow(
              column(width=9,
                     div(style="width:100% ; max-width: 1200px",
                         
                         tabBox(title="Download / Install SHAMAN", id="tabset1", width=NULL,
                                tabPanel("HOWTO", tags$script(type="text/javascript", language="javascript", src="google-analytics.js"),
                                         p("SHAMAN is available for R>3.X. The installation, download and execution can all be performed with a small R script :",style = "font-family: 'times'; font-si16pt"),
                                         wellPanel("# Load shiny packages",br(),
                                           "if(!require('shiny')){",br(),"  install.packages('shiny')",br(),"  library(shiny)",br(),"}",br(),
                                              br(),"# Install dependencies, download last version of SHAMAN from github and run shaman in one command :",br(),"runGitHub('aghozlane/shaman')"),
                                         p("This script can also be dowloaded", a("here", target="_blank", href="shamanapp.R"), "and executed as following :"),
                                         wellPanel("chmod +x ./shamanapp.R && Rscript ./shamanapp.R"),
                                         p("Contribution to SHAMAN code are always welcome and can be performed with the", a("github deposit.",href="https://github.com/aghozlane/shaman"))
                                ))
                         )
                     )
              )
            ),
    
stevenn's avatar
stevenn committed
201
202
203
    tabItem(tabName = "Upload",
            tags$style(type='text/css', ".well { max-width: 20em; }"),
            fluidRow(
Stevenn Volant's avatar
Stevenn Volant committed
204
205
206
207
208
209
210
              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,
211
                  selectInput("FileFormat","",c("Count table & taxonomy"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts")
Stevenn Volant's avatar
Stevenn Volant committed
212
                ),
stevenn's avatar
stevenn committed
213
                conditionalPanel(condition="input.FileFormat=='fileCounts'",
214
                  box(title="Load the count table",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
215
216
217
218
                      fluidRow(
                        column(width=6,radioButtons("TypeTable",h6(strong("Type:")),c("OTU/Gene table"="OTU","MGS table"="MGS")))
                      ),
                      fileInput('fileCounts', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
219
                  ),
stevenn's avatar
stevenn committed
220
                  
Stevenn Volant's avatar
Stevenn Volant committed
221
222
223
224
225
226
227
                  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
228
                      fileInput('fileTaxo', h6(strong('Select your file')),width="100%")
stevenn's avatar
stevenn committed
229
230
231
232
233
                  )
                  
                ),
                
                conditionalPanel(condition="input.FileFormat=='fileBiom'",
Stevenn Volant's avatar
Stevenn Volant committed
234
                                 box(title="Load the BIOM file",width = 3,height = "250px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
stevenn's avatar
stevenn committed
235
236
237
                                     fileInput('fileBiom', h5(strong('Select your file')),width="100%")
                                 )           
                )
Stevenn Volant's avatar
Stevenn Volant committed
238
             ),
stevenn's avatar
stevenn committed
239
240
241
              column(12,uiOutput("TabBoxData"))

              
Stevenn Volant's avatar
Stevenn Volant committed
242
          
stevenn's avatar
stevenn committed
243
244
    ),
    
stevenn's avatar
stevenn committed
245
246
247
  #### Statistical analysis

    tabItem(tabName = "RunDiff",
stevenn's avatar
stevenn committed
248
            fluidRow(
249
250
              column(width=3,valueBoxOutput("RowTarget",width=NULL)),
              #column(width=3,infoBoxOutput("RowTarget",width=NULL)),
stevenn's avatar
stevenn committed
251
              column(width=3,infoBoxOutput("InfoTaxo",width=NULL)),
252
              column(width=3,infoBoxOutput("InfoDESeq",width=NULL)),
253
              column(width=3,infoBoxOutput("InfoContrast",width=NULL))
Stevenn Volant's avatar
Stevenn Volant committed
254
            ),            
stevenn's avatar
stevenn committed
255
            fluidRow(
stevenn's avatar
stevenn committed
256
257
258
              column(width=5,
                box(title="Experimental design",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
                  fluidRow(
stevenn's avatar
stevenn committed
259
260
                    column(width=6,fileInput('fileTarget', h6(strong('Select your target file')),width="100%")),
                    column(width=6,uiOutput("SelectTaxo"))
stevenn's avatar
stevenn committed
261
262
263
264
                  ),
                  fluidRow( 
                    column(width=6,uiOutput("SelectInterestVar")),
                    column(width=6,uiOutput("SelectInteraction2")),
265
                    column(width=6,uiOutput("RunButton"))
stevenn's avatar
stevenn committed
266
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
267
268
269
                ),
                uiOutput("BoxTarget"),
                uiOutput("BoxCountsMerge")
stevenn's avatar
stevenn committed
270
              ),
stevenn's avatar
stevenn committed
271
272
273
       
              column(width=7,
                box(title="Options",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
svolant's avatar
svolant committed
274
275
                    p(strong("Linear model options"),Align ="center"),
                    hr(),
stevenn's avatar
stevenn committed
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
                  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
292
                           radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='Auto',"No cut-off"=Inf,"Value"="val")),
stevenn's avatar
stevenn committed
293
294
295
296
297
298
299
300
                           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"))
svolant's avatar
svolant committed
301
                    )
302
                    # column(width=3,uiOutput("RefSelect"))
303
                  ),
svolant's avatar
svolant committed
304
305
                  p(strong("Options for the normalization step"),Align ="center"),
                  hr(),
306
                  fluidRow(
svolant's avatar
svolant committed
307
308
                    column(width=3,checkboxInput("AccountForNA","Compute geometric mean without 0",value=TRUE)),
                    column(width=3,uiOutput("SelectVarNorm")),
309
310
311
312
                    column(width=3,
                        fileInput('fileSizeFactors', h6(strong('Define your own size factors')),width="100%")
                    ),
                    column(width=3,br(),htmlOutput("InfoSizeFactor"))
stevenn's avatar
stevenn committed
313
                  )
stevenn's avatar
stevenn committed
314
                ),
315
316
                fluidRow(
                column(width=8,
317
                        uiOutput("contrastBox"),
318
319
320
321
                       uiOutput("contrastBoxAdvanced")
                       ),
                column(width=4,
                       uiOutput("contrastDefined")
322
323
                )
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
324
              )
stevenn's avatar
stevenn committed
325
            )
stevenn's avatar
stevenn committed
326
    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
327
    tabItem(tabName = "DiagPlotTab",
stevenn's avatar
stevenn committed
328
            fluidRow(
stevenn's avatar
stevenn committed
329
              column(width=9,
svolant's avatar
svolant committed
330
331
332
333
334
                     tags$head(tags$style(HTML(spincss))),
                     div(id = "plot-container",
                         tags$img(src = "gears.gif",id ="loading-spinner"),
                         plotOutput("PlotDiag",height="100%")
                     ),
Stevenn Volant's avatar
Stevenn Volant committed
335
                br(),
336
                conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
stevenn's avatar
stevenn committed
337
                  box(title = "Size factors",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
338
339
                    dataTableOutput("SizeFactTable"),
                    downloadButton('ExportSizeFactor', 'Export table')
stevenn's avatar
stevenn committed
340
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
341
342
343
344
                ),
                  
                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
345
                                    plotOutput("PlotEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
346
347
348
349
                                 )
                ),
                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
350
                                     plotOutput("PlotpcoaEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
351
                                 )
stevenn's avatar
stevenn committed
352
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
353
                
stevenn's avatar
stevenn committed
354
355
              ),
              column(width=3,
356
357
                box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
                  selectInput("DiagPlot","",c("Total barplot"="barplotTot","Nul barplot"="barplotNul",
358
                                              "Maj. taxonomy"="MajTax","Boxplots" = "boxplotNorm", "Density"="densityPlot", "Dispersion" = "DispPlot",
359
                                              "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","Clustering" = "clustPlot"))
360
                    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
361
                box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
362
                    conditionalPanel(condition="input.DiagPlot!='clustPlot' && input.DiagPlot!='pcaPlot' && input.DiagPlot!='SfactorsVStot' && input.DiagPlot!='DispPlot'",
363
                                     radioButtons("CountsType","Counts:",c("Normalized"="Normalized","Raw"="Raw"),inline = TRUE)
364
                                     ),
365
366
367
                    conditionalPanel(condition="input.DiagPlot=='boxplotNorm'",
                                    checkboxInput("RemoveNullValue","Remove 0",value = TRUE)
                                    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
368
                    conditionalPanel(condition="input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntDiag")),
369
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='pcaPlot'",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
370
                                     h5(strong("Select the modalities")),
svolant's avatar
svolant committed
371
372
373
374
375
376
                                     uiOutput("ModMat"),
                                     fluidRow(
                                       column(width=5,uiOutput("PC1_sel")),
                                       column(width=2,br(),br(),p("VS")),
                                       column(width=5,uiOutput("PC2_sel"))
                                     )
377
                                    ),
Stevenn Volant's avatar
Stevenn Volant committed
378
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='SERE' || input.DiagPlot=='clustPlot' ",
379
380
                                      selectInput("DistClust","Distance",c("euclidean", "SERE"="sere", "canberra", "bray", "kulczynski", "jaccard", 
                                                  "gower", "altGower", "morisita", "horn","mountford","raup","binomial",
381
                                                  "chao","cao","mahalanobis"),selected="canberra")
382
                                    )
Stevenn Volant's avatar
Stevenn Volant committed
383
                    
svolant's avatar
svolant committed
384

stevenn's avatar
stevenn committed
385
386
387
388
389
390
391
#                 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,
392
393
394
395
#                     conditionalPanel(condition="input.DiagPlot=='Sfactors'",
#                                      h6(strong("Layout")),
#                                      numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
#                     ),
Stevenn Volant's avatar
Stevenn Volant committed
396
397
                  sliderInput("heightDiag", "Height",min=100,max=1500,value = 500,step =10),

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
398
399
400
401
402
403
404
405
406
407
408
409
                  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
410
411
412
413
414
415
416
                  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)),
417
                    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
418
419
420
                    
                  )

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
421
422
#                   sliderInput("widthDiag", "width",min=100,max=1500,value = 1000,step =10)
                 
stevenn's avatar
stevenn committed
423

stevenn's avatar
stevenn committed
424
425
426
427
428
429
430
431
432
433
434
435
436
437
              ),
              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
438
439
440
              )
            )
        )
stevenn's avatar
stevenn committed
441
442
443
    ),
    tabItem(tabName = "TableDiff",
            fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
444
445
446
447
448
              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")
449
450
451
452
453
                     ),
                     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
454
            )
Stevenn Volant's avatar
Stevenn Volant committed
455
            ) 
stevenn's avatar
stevenn committed
456
457
458
459
    ),
  
  #### Data Viz
  
460
  tabItem(tabName = "GlobVisu",
stevenn's avatar
stevenn committed
461
          fluidRow(
462
            column(width=9,
svolant's avatar
svolant committed
463
464
465
466
467
468
469
470
                   tags$head(tags$style(HTML(spincss))),
                   div(id = "plot-container",
                       conditionalPanel(condition="input.PlotVisuSelect=='Boxplot' || input.PlotVisuSelect=='Diversity' || input.PlotVisuSelect=='Rarefaction'",   
                                          tags$img(src = "gears.gif",id ="loading-spinner")
                                        ),
                       uiOutput("plotVisu")
                   ),
                   
svolant's avatar
svolant committed
471
                   
472
                   ### Regression and correlation outputs for the scatter plot
svolant's avatar
svolant committed
473
                   conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot' && input.AddRegScatter", 
svolant's avatar
svolant committed
474
475
476
477
478
479
                                    fluidRow(
                                      column(width=6,
                                      br(),
                                      box(title = "Regression coefficients",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                                          dataTableOutput("lmRegScatter")
                                      )
svolant's avatar
svolant committed
480
481
                                    ),
                                    column(width=6,br(),htmlOutput("lmEquation"))
svolant's avatar
svolant committed
482
                                    )
483
484
485
486
487
488
489
490
491
492
493
494
495
                   ),
                   conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot'",
                                    useShinyjs(),
                                    br(),
                                    p(actionButton("scatterD3-reset-zoom", HTML("<span class='glyphicon glyphicon-search' aria-hidden='true'></span> Reset Zoom")),Align="right"),
                                    box(title = "Correlation table",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                                        dataTableOutput("CorTable")
                                    )
                   ),
                   
                   ## Values of the diversities
                   conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
                                    br(),
svolant's avatar
svolant committed
496
                      box(title = "Diversity values",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
497
498
499
500
501
                                    dataTableOutput("Diversitytable"),
                                    downloadButton('ExportDiversitytable', 'Export table')
                          
                      )
                   ) 
svolant's avatar
svolant committed
502
503
                                    
                   ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
504
505

            column(width=3,
506
              box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
svolant's avatar
svolant committed
507
                  selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction"),selected = "Barplot")
508
              ),
509
510


511
512
513
514
515
              ########################################################################
              ###
              ###               Options Visualization
              ###
              ########################################################################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
516
              box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
svolant's avatar
svolant committed
517
518
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Scatterplot' ",
                                   uiOutput("VarIntVisu"),
519
520
                                   h5(strong("Select the modalities")),
                                   uiOutput("ModVisu")
521
                  ),
svolant's avatar
svolant committed
522
523
                  conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot' ",
                                   uiOutput("VarIntVisuScatter"),
524
525
                                   radioButtons("TransDataScatter","Data transformation",c("Log2 +1" = "log2","None" = "none"),inline=TRUE),
                                   hr(),
svolant's avatar
svolant committed
526
                                   radioButtons("CorMeth","Correlation method",c("Pearson" = "pearson","Spearman" = "spearman"),inline=TRUE),
svolant's avatar
svolant committed
527
528
529
                                   checkboxInput("AddRegScatter","Add regression line",FALSE)
                  ),                 
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot'",
svolant's avatar
svolant committed
530
                                   radioButtons("SelectSpecifTaxo","Select the features",c("Most abundant"="Most","All"="All", "Differential features" = "Diff", "Non differential features" = "NoDiff"))
531
                  ),
svolant's avatar
svolant committed
532
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot' && (input.SelectSpecifTaxo=='Diff' || input.SelectSpecifTaxo=='NoDiff') ",
533
534
                                   selectizeInput("ContrastList_table_Visu","",choices = "", multiple = TRUE),
                                   radioButtons("UnionInterContrasts","Union or intersection ?",c("Union"="Union","Intersection"="Inter"),inline = TRUE)
535
                  ),
svolant's avatar
svolant committed
536
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot'",
537
538
539
540
541
542
543
                                   uiOutput("TaxoToPlotVisu")
                  ),

                ##################
                ## BARPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Barplot'",
544
                                 hr(),
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
                                 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 = "scaleHeatmap",label = h6(strong("Scale:")),choices = c("None" = "none", "Rows" = "row", "Column" = "col"),selected = "none")
                                 
                ),
                
                ##################
                ## BOXPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Boxplot'",
561
                                 hr(),
562
563
564
565
566
567
568
                                 selectizeInput("typeDataBox",h6(strong("Type of data")),c("Log2"="Log2","Relative"="Relative"))
                ),
                
                ##################
                ## DIVERSITY
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
569
570
571
572
                                 selectizeInput("WhichDiv",h6(strong("Diversity")),c('Alpha','Beta','Gamma','Shannon','Simpson','Inv.Simpson'),selected  = c('Alpha','Shannon','Simpson','Inv.Simpson'),multiple=TRUE)
                ),
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
                                 uiOutput("SelectVarBoxDiv")
573
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
574
              ),
575
576


577
578
579
580
581
              ########################################################################
              ###
              ###               Appearance Visualization
              ###
              ########################################################################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
582
              box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
583
                sliderInput("heightVisu", h6(strong("Height")),min=100,max=4000,value = 800),
584
585
586
587
                ##################
                ## BOXPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Boxplot'",
588
                                 uiOutput("ColBoxplot"),
Stevenn Volant's avatar
Stevenn Volant committed
589
                                 radioButtons("ScaleBoxplot","Scales",c("Fixed"="fixed","Free"="free"),inline=TRUE),
590
591
592
593
594
595
                                 checkboxInput("CheckAddPointsBox","Add points",value=TRUE)
                ),
                ##################
                ## DIVERSITY
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
596
597
                                 radioButtons("DivScale","Scales",c("Fixed"="fixed","Free"="free"),selected = "free",inline=TRUE),
                                radioButtons("DivAddError","Add Error bars",c("Add"="Add","Remove"="Remove"),selected = "Add",inline=TRUE)
598
599
600
601
                ),
                ##################
                ## HEATMAP
                ##################
602
                conditionalPanel(condition="input.PlotVisuSelect=='Heatmap'",
Stevenn Volant's avatar
Stevenn Volant committed
603
                                 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")
604
605
606
607
608
609
610
611
612
613
614
615
                ),
                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))
                                 )
616
                ),
svolant's avatar
svolant committed
617
618
619
620
621
622
623
624
625
626
                
                ##################
                ## Scatterplot
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot'",
                                 fluidRow(
                                   column(width=12,sliderInput("SizeLabelScatter", h6("Label size"),min=0,max=50,value = 10,step = 1))
                                  )
                ),
                
627
628
629
                ##################
                ## ALL
                ##################
630
                conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Scatterplot'",
631
632
                                 radioButtons(inputId = "SensPlotVisu",label = h6(strong("Orientation")),choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical",inline = TRUE)
                )
Stevenn Volant's avatar
Stevenn Volant committed
633
634
635
636
637
638
639
640
641
642
643
644
645
646
              ),
              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")
647
              )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
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
  tabItem(tabName = "CompPlot",
          fluidRow(
            column(width=9,
                   uiOutput("plotVisuComp"),
                   conditionalPanel(condition="input.PlotVisuSelectComp=='Venn'",
                                    dataTableOutput("DataVenn")
                   )
            ),
            column(width=3,
                   box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
                        selectizeInput("PlotVisuSelectComp","",c("Venn diagram"="Venn","Heatmap"="Heatmap_comp"),selected = "Heatmap_comp")
                   ),
                   box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                          selectizeInput("ContrastList_table_FC",h6(strong("Contrasts (Min = 2)")),choices = "", multiple = TRUE),
                          conditionalPanel(condition="input.PlotVisuSelectComp=='Heatmap_comp'",
                                          radioButtons("SelectSpecifTaxoComp","Select the features",c("Most abundant"="Most","All"="All", "Differential features" = "Diff", "Non differential features" = "NoDiff"))
                                          ),
                          conditionalPanel(condition="input.PlotVisuSelectComp=='Heatmap_comp' && (input.SelectSpecifTaxoComp=='Diff' || input.SelectSpecifTaxoComp=='NoDiff')",
                                          selectizeInput("ContrastList_table_VisuComp","",choices = "", multiple = TRUE),
                                          radioButtons("UnionInterContrastsComp","Union or intersection ?",c("Union"="Union","Intersection"="Inter"),inline = TRUE)
                                          ),
                          conditionalPanel(condition="input.PlotVisuSelectComp=='Heatmap_comp'",
                                          uiOutput("TaxoToPlotVisuComp"),
                                          selectizeInput(inputId = "scaleHeatmapComp",label = h6(strong("Scale:")),choices = c("None" = "none", "Rows" = "row", "Column" = "col"),selected = "none"),
                                          selectInput("SortHeatComp","Sort by:", c("Selection" ="Selection","Values" = "Values","Names"="Names","Auto"="Auto"))
                                          )
                    ),
                   
                   box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                       sliderInput("heightVisuComp", h6(strong("Height")),min=100,max=4000,value = 800),
                       
                       ##################
                       ## HEATMAP
                       ##################

                       conditionalPanel(condition="input.PlotVisuSelectComp=='Heatmap_comp'",
                                        radioButtons(inputId = "SensPlotVisuComp",label = h6(strong("Orientation")),choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical",inline = TRUE),
                                        fluidRow(
                                          column(width=12,h6(strong("Labels options"))),
                                          column(width=6,sliderInput("LabelSizeHeatmapComp", h6("Size"),min=0.1,max=2,value = 0.7,step = 0.1)),
                                          column(width=6,sliderInput("LabelOrientHeatmapComp", h6("Orientation"),min=0,max=90,value = 0,step = 5)),
                                          column(width=6,sliderInput("LabelColOffsetHeatmapComp", h6("Column offset"),min=0,max=4,value = 0,step = 0.5)),
                                          column(width=6,sliderInput("LabelRowOffsetHeatmapComp", h6("Row offset"),min=0,max=4,value = 0,step = 0.5)),
                                          column(width=12,h6(strong("Margins options"))),
                                          column(width=6,sliderInput("rightMarginComp", h6("Right"),min=0,max=20,value = 6,step = 1)),
                                          column(width=6,sliderInput("lowerMarginComp", h6("Lower"),min=0,max=20,value = 6,step = 1))
                                        )
                       )
                       
                    ),
                   conditionalPanel(condition="input.PlotVisuSelectComp!='Venn'",
                     box(title = "Export",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
                         ##################
                         ## BARPLOT
                         ##################
                         selectInput("Exp_format_VisuComp",h5(strong("Export format")),c("png"="png","pdf"="pdf","eps"="eps","svg"="svg"), multiple = FALSE),
                         fluidRow(
                           column(width=6,numericInput("heightVisuExportComp", "Height (in px)",min=100,max=NA,value = 500,step =1)),
                           column(width=6,numericInput("widthVisuExportComp", "Width (in px)",min=100,max=NA,value = 500,step =1))
                         ),
                         downloadButton("exportVisuComp", "Export")
                     )
                   )
                   
                   
            )
          )
  ),

stevenn's avatar
stevenn committed
721
722
  #### Krona plot
  tabItem(tabName = "Krona",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
723
         fluidRow(
Stevenn Volant's avatar
Stevenn Volant committed
724
725
726
727
728
729
730
731
732
733
734
735
            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!")
            )
736
        )
Stevenn Volant's avatar
Stevenn Volant committed
737
 #includeHTML("file:///home/aghozlan/workspace/SHAMAN_App/www/text.krona.html")
stevenn's avatar
stevenn committed
738
  )
739
 )
svolant's avatar
svolant committed
740
)
741
742
)
  ## GOOGLE ANALYTIC
743
 #tags$head(includeScript("google-analytics.js"))
Stevenn Volant's avatar
logo    
Stevenn Volant committed
744
745
746
747
  ## Logo SHAMAN
  dbHeader <- dashboardHeader(title = "SHAMAN")
  dbHeader$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
748
# Put them together into a dashboardPage
svolant's avatar
svolant committed
749
750

    dashboardPage(skin="blue",
Stevenn Volant's avatar
logo    
Stevenn Volant committed
751
752
753
754
    dbHeader,
    sidebar,
    body
  )
svolant's avatar
svolant committed
755
}
stevenn's avatar
stevenn committed
756
757


svolant's avatar
svolant committed
758