ui.R 68.7 KB
Newer Older
svolant's avatar
svolant committed
1
function(request) {
stevenn's avatar
stevenn committed
2
sidebar <- dashboardSidebar(
svolant's avatar
svolant committed
3
4
  useShinyjs(),
  inlineCSS(appCSS),
5
6
7
#   tags$head(
#     tags$script(src = "custom.js")
#   ),
svolant's avatar
svolant committed
8
9
10
11
  div(id = "loading-content-bar",
      p()),
  div(
    id = "app-content-bar",
svolant's avatar
svolant committed
12
  sidebarMenu(id = "side",
stevenn's avatar
stevenn committed
13
    menuItem("Home", tabName = "Home", icon = icon("home")),
14
    menuItem("Tutorial", tabName = "Tutorial", icon = icon("book")),
15
    menuItem("Download/Install", tabName = "Download", icon = icon("download")),
16
    menuItem("Raw data", tabName = "RawData", icon = icon("upload")),
stevenn's avatar
stevenn committed
17
    menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
svolant's avatar
svolant committed
18
    # bookmarkButton(),
Stevenn Volant's avatar
logo    
Stevenn Volant committed
19
    menuItemOutput("dymMenu"),
svolant's avatar
svolant committed
20
    
Stevenn Volant's avatar
Stevenn Volant committed
21
    img(src = "logo.jpg", height = 49, width = 220,style="position:absolute;bottom:0;margin:0 0 15px 10px;")
stevenn's avatar
stevenn committed
22
  )
svolant's avatar
svolant committed
23
  )
stevenn's avatar
stevenn committed
24
25
26
)

body <- dashboardBody(
svolant's avatar
svolant committed
27
28
29
30
31
32
33
34
35
36
37
38
  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
39
40
  tabItems(
    tabItem(tabName = "Home",
svolant's avatar
svolant committed
41
42
            fluidRow(
              column(width=9,
43
            div(style="width:100% ; max-width: 1200px; height: 550px",
svolant's avatar
svolant committed
44
                
45
              tabBox(title="Welcome to SHAMAN", id="tabset1", width=NULL,
46
47
                   # tags$script(type="text/javascript", language="javascript", src="google-analytics.js"),
                   tabPanel("About", 
48
                            p("SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization,
Stevenn Volant's avatar
Stevenn Volant committed
49
                                       the differential analysis and mutiple visualization.",style = "font-family: 'times'; font-si16pt"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
50
51
                            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
52
                              Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995].
53
                              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/"), ".
54
                              A presentation about SHAMAN is available", a("here",target="_blank",href="shaman_presentation.pdf")," and a poster", a("here.",target="_blank",href="shaman_poster.pdf"), br(),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
55
                              "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
56
                            p("Hereafter is the global workflow of the SHAMAN application:"),
svolant's avatar
svolant committed
57
                            div(img(src = "Workflow_sh.png",width = "100%",height = "100%",style="max-width: 800px;"),Align="center")
Stevenn Volant's avatar
Stevenn Volant committed
58
                            ),
Stevenn Volant's avatar
Stevenn Volant committed
59
                   tabPanel("Authors", h3("The main contributors to SHAMAN:"),
Stevenn Volant's avatar
Stevenn Volant committed
60
                            p(a("Stevenn Volant", href="mailto:stevenn.volant@pasteur.fr"), "(Initiator, coding, testing, documentation, evaluation)"),
61
                            p(a("Amine Ghozlane",href="mailto:amine.ghozlane@pasteur.fr"), "(Coding, testing, documentation, evaluation, packaging)"),
62
                            p("Pierre Lechat", "(Coding, testing, feature suggestions)"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
63
                            p("Hugo Varet", "(Coding, testing, feature suggestions)"),
64
65
66
                            p("Christophe Malabat", "(Packaging)"), 
                            p("Marie-Agnès Dillies", "(Evaluation)"),
                            p("Sean Kennedy", "(Evaluation)"),
Stevenn Volant's avatar
Stevenn Volant committed
67
68
                            h3("Acknowledgements"),
                            p("Thanks to the following people for patches and other suggestions for improvements:"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
69
                            p("Carine Rey, ","Alexis Criscuolo, ","Julien Tap, ","Anna Zhukova, ", "Rachel Torchet.")
Stevenn Volant's avatar
logo    
Stevenn Volant committed
70
                          ),
71
72
73
                   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
74
                   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"),
75
                   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
76
77
78
79
            )))),
              column(width=3,
            box(
              title = "What's new in SHAMAN", width = NULL, status = "primary",
80
              div(style = 'overflow-y: scroll; height: 550px',
81
                  addNews("March 30th 2017","Krona, Phylogeny and bug fixes","Krona and phylogenetic tree plots are now available in visualisation. Several new distance are available in PCOA. The import float count matrices is now ok. We have finaly debugged the export of the relative abundance/normalized matrices."),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
82
                  addNews("Dec 9th 2016","Phylogenetic tree and stress plot","You can now upload a phylogenetic tree to calculate the unifrac distance (only available at the OTU level). 
svolant's avatar
svolant committed
83
                          The stress plot has been added to evaluate the goodness of fit of the NMDS."),
84
                  addNews("Nov 22th 2016","New visualization and bug fix","We have implemented a new visualization called tree abundance. Some bugs have been fixed (thanks Carine Rey from ENS)."),
85
                  addNews("Oct 12th 2016","Filtering step and bugs fix","You can now apply a filter on the features according to their abundance 
86
                          and the number of samples. Bugs on confidence intervals for the alpha diversity have been fixed."),
87
                  addNews("Sep 21th 2016","SHAMAN on docker","The install of SHAMAN is now available with docker.
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
88
                           The R install is also updated and passed in release candidate state."),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
89
                  addNews("Sep 14th 2016","Download and install SHAMAN","You can install SHAMAN (beta)."),
svolant's avatar
svolant committed
90
91
92
                  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 
93
                                                                have been added to compare the results of 2 or more contrasts."), 
svolant's avatar
svolant committed
94
                  addNews("Jun 17th 2016","Diversity plots","Enhancement of the visualtisation of the diverties. 
95
                                                              The shanon and inv. shanon have been added.")
svolant's avatar
svolant committed
96
97
98
99
                  )
            )
              )
              )
100
    ),
Stevenn Volant's avatar
Stevenn Volant committed
101

102
    tabItem(tabName = "Tutorial",
103
104
            div(style="width:100% ; max-width: 1200px",
            tabBox(title="How to use SHAMAN", id="tabset1", width =NULL,
105
106
107
108
109
            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(),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
110
              "- the otu annotation table : Alimintest_otu_annotation.csv,", br(),
111
112
              "- the experimental design : Alimintest_target.csv,", br(),
              "- the contrast table : Alimintest_contrasts.csv."),
113
114
            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"),
115
116
117
            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",
118
            p("The first step consists to load the count table and the annotation table as follow :"),
119
            p("- Select 'Upload your data'", br(),
120
121
              "- 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(),
122
              "- When successfully loaded, the tables are accessible as bellow :",br(),
123
              img(src = "tutorial/tutorial_upload3.png",width = "100%",style="max-width: 600px"),img(src = "tutorial/tutorial_upload4.png",width = "100%",style="max-width: 600px"))),
124
            tabPanel("2-Differential analysis",
125
            p("The second step consists to load the experimental design and the contrast table as follow :"),
126
            p("- Select 'Run differential analysis'",br(),
127
128
129
130
131
132
133
              "- 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"))),
134
            tabPanel("3-Diagnostic plots",
135
136
137
138
139
140
141
142
143
            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"))),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
144
145
146
147
148
            tabPanel("4-Tables",
                     p("'Tables' section provides the results of the differential analysis.
                       For one given contrast, we have:",br(),
                       "- The id of the given taxonomical level",br(),
                       "- The base mean is the mean normalized count for the given annotation of all samples.",br(),
149
150
151
                       "- The fold-change is a mesure describing how much the abundance varies from one condition to an other. For instance, if the abundance is 100 in condition 1 and 200 for condition 2, the fold-change equals 100/200=0.5.",br(),
                       "- The log2 fold-change is the log2 value of the fold-change.",br(),
                       "- The p-value adjusted (padj) is the pvalue obtained by the Wald test and adjusted by Benjamini & Hochberg procedure (BH) or Benjamini & Yekutieli procedure (see linear model options).",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
152
            img(src = "tutorial/tutorial_table.png",width = "100%",style="max-width: 900px"))),
153
154
            tabPanel("5-Visualization",
                     p("'Diagnostic plots' section provides several visualization to control the analysis",br(),
155
156
157
158
                     "- 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
159
160
                     "- Rarefaction",br(),img(src="tutorial/tutorial_rarefaction.png",width = "100%",style="max-width: 900px"))),
            tabPanel("6-Other datasets available",
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
            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"))
              ))
184
    ),
Stevenn Volant's avatar
Stevenn Volant committed
185
    
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
186
187
188
189
190
191
    tabItem(tabName = "Download",
            fluidRow(
              column(width=9,
                     div(style="width:100% ; max-width: 1200px",
                         
                         tabBox(title="Download / Install SHAMAN", id="tabset1", width=NULL,
192
                                tabPanel("Docker install",
193
194
195
                                p("Docker install is the easiest way to use SHAMAN locally."),
                                p("- Install docker on ubuntu (Linux):",a("here",href="https://docs.docker.com/engine/installation/linux/ubuntulinux/")),
                                p("- Install docker on Windows and Mac:"),
196
197
198
199
                                p("Download and install docker from",a("https://www.docker.com/", href="https://www.docker.com/"),
                                  "Then, you will need to install the", a("Docker toolbox.", href="https://www.docker.com/products/docker-toolbox"),
                                  "Once installed, run ‘Docker Quickstart Terminal’ application."),
                                p("- Running SHAMAN:"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
200
                                wellPanel(div(style = 'max-width: 900px',"docker pull aghozlane/shaman && docker run --rm -p 80:80 -p 5438:5438 aghozlane/shaman")),
201
202
                                p("Then connect to http://0.0.0.0/ with your favorite web navigator."),
                                p("Failed: port is already allocated ?"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
203
                                wellPanel(div(style = 'max-width: 900px',"docker run --rm -p 3838:80 -p 5438:5438 aghozlane/shaman")),
204
205
                                p("Then connect to http://0.0.0.0:3838/."),
                                p("- Docker update after an update of SHAMAN:"),
206
                                wellPanel(div(style = 'max-width: 900px',"docker pull aghozlane/shaman"))
207
                                ),
208
                                tabPanel("R install (RC)",
209
                                         p("SHAMAN is available for R>3.1.2. The installation, download and execution can all be performed with a small R script :",style = "font-family: 'times'; font-si16pt"),
210
                                         wellPanel(div(style = 'max-width: 900px',"# Load shiny packages",br(),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
211
                                           "if(!require('shiny')){",br(),"  install.packages('shiny')",br(),"  library(shiny)",br(),"}",br(),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
212
                                           "system(\"Rscript -e 'library(\\\"shiny\\\");runGitHub(\\\"pierreLec/KronaRShy\\\",port=5438)'\",wait=FALSE)",
213
                                              br(),"# Install dependencies,",br(),"# download last version from github,",br(),"# and run SHAMAN in one command:",br(),"runGitHub('aghozlane/shaman')")),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
214
                                         p("This script can also be dowloaded", a("here", target="_blank", href="shamanapp.R"), "and executed as following :"),
215
                                         wellPanel(div(style = 'max-width: 900px',"chmod +x ./shamanapp.R && Rscript ./shamanapp.R")),
216
                                         p("Of note, the R version has an impact on the contrast definition. DESeq2 contrast are harder to define on R>3.2."),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
217
218
219
220
221
222
                                         p("Contribution to SHAMAN code are always welcome and can be performed with the", a("github deposit.",href="https://github.com/aghozlane/shaman"))
                                ))
                         )
                     )
              )
            ),
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
    tabItem(tabName = "RawData",
                        tags$style(type='text/css', ".well { max-width: 20em; }"),
                        fluidRow(
                          HTML('<center><h1>MASQUE : Metagenomic Analysis with a Quantitative pipeline</h1></center>'),

                          column(width=8,
                            div(style="background-color: white; padding-left:20px;",
                            HTML('
                           <h2>Introduction</h2>

                                 <p>The aim of this part is to provide an easy cluster interface to perform <b>targeted metagenomic analysis</b>. This analysis will be done using the MASQUE pipeline which allows :</p>

                                 <ul>
                                 <li>to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.</li>
                                 <li>to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.</li>
                                 <li>to perform an "uptodate" analysis considering the scientific litterature.</li>
                                 </ul>

                                  <hr></hr>
                                 <h2>Process</h2>

                                 <p>We follow the recommandation described by Robert C. Edgar in <a href="http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2604.html" target="_blank" >Uparse</a> supplementary paper.<br>
                                   The clustering process in MASQUE is performed as the following :<br>
                                   1.  Read quality control<br>
                                   2.  Dereplication<br>
                                   3.  Chimera filtering<br>
                                   4.  Clustering<br>
                                   5.  Realignment/mapping<br>
                                   6.  Taxonomical annotation of the OTU<br>
                                   7.  Quality check of every step  </p>

                                   <p>You can find more information in the presentation <a href="/aghozlane/masque/blob/master/tp/Targeted_metagenomics.pdf">here</a>. We try to describe the idea behind each step and a complete TP to do it on your own.</p>'
                              )
            #
            #
            #                      <\ui> to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.
            #                      to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.
            #                      to perform an uptodate analysis considering the scientific litterature."
svolant's avatar
svolant committed
261
262
263
264
265
266
                          )),
            
            column(width=4,
                   gaugeOutput("gaugeMasque", width = "100%", height = "100%")
                   )
            ),
svolant's avatar
svolant committed
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
            
            hr(),
            HTML('<center><h2 style="color:#053383;"><b>Start your analysis</b></h2></center>'),
            hr(),
            fluidRow(
              column(width=2),
              column(width=8,
              box(title="About",width = 12, status = "primary",
  
                  column(width=6,  radioButtons("DataTypeMasque",label = "Type of data",choices = c("16S/18S" = "16S_18S","23S/28S" = "23S_28S","ITS" = "ITS"),inline = TRUE)),
                  column(width=6,  radioButtons("PairedOrNot",label = "Paired-end sequencing ?",choices = c('Yes'="y","No"="n"),selected = "n",inline = TRUE)),
                  column(width=6,  tags$div(title="Enter a valid email address to get your results",textInput("to", "Email address *", value="yyy@xxx"))),
                  column(width=6,  selectizeInput("HostName",label = "Select the host",
                                                  choices =   c("None"="", "a.stephensi (mosquito)" = "astephensi"," b.taurus (cow)" = "btaurus", "c.familiaris (dog)" = "cfamiliaris",
                                                                "chiroptera (bat)" = "chiroptera", "c.sabaeus (Apes)" = "csabaeus" , "d.melanogaster (fly)"="dmelanogaster", 
                                                                "e.caballus (Horse)" = "ecaballus", "f.catus (cat)" = "fcatus", "hg18 (human)"="hg18", "hg19 (human)"="hg19", 
                                                                "hg38 (human)" = "hg38", "m.lucifugus (bat)" = "mlucifugus", "mm8 (mouse)"= "mm8", "mm9 (mouse)" = "mm9", 
                                                                "mm10 (mouse)"="mm10", "p.vampyrus (bat)" = "pvampyrus", "s.scrofa (Boar)" = "sscrofa"))),
                  column(width=6, tags$div(title="If no, default values are chosen",checkboxInput("primer", "Specify the primer"))),
                  conditionalPanel(condition="input.primer && input.PairedOrNot=='y'",
                                   column(width=12,
                                     textInput("R1primer",label = "Forward primer",value = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG"),
                                     textInput("R2primer",label = "Reverse primer",value = "GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC")
                                   )
                  ),
                  conditionalPanel(condition="input.primer && input.PairedOrNot=='n'",
                                   column(width=12,
                                     textInput("primerSingle",label = "Primer",value = "TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG")
                                   )
                  )
              ), 
              
              box(title="Directory containing the FastQ files ",width = 12, status = "primary",
                    column(width=12,verbatimTextOutput("dirSel")),
                    br(),
                    column(width=12,
                            shinyDirButton("dir", "Select a directory", "Upload",buttonType = "primary"),
                            HTML("&nbsp;"),
                            actionButton("LoadFiles",'Load',icon=icon("refresh"))
                    ),
                    conditionalPanel(condition="input.LoadFiles>=1",
                                     br(),
                                     hr(),
                                     br(),
                                      column(width=12,uiOutput("FastQList_out"))
                                     )
                    
              ),
315

svolant's avatar
svolant committed
316
317
318
319
320
321
322
323
324
325
326
327
328
329
              box(id="box-match",title=" Match the paired files (only for paired-end sequencing)",width = 12, status = "primary",
                      column(width=6,  textInput("R1files",label = "Suffix R1 (Forward)",value = "_R1"),
                            selectInput("R1filesList",label = "","",multiple =TRUE,selectize=FALSE)),
                            column(width=6,  
                                    textInput("R2files",label = "Suffix R2 (Reverse)",value = "_R2"),
                                    selectInput("R2filesList",label = "","",multiple =TRUE,selectize=FALSE)
                                   ),
                            column(width=12,
                                    actionButton("MatchFiles_button",'Match',icon=icon("exchange"),class="btn-primary",style="color: #fff;"),
                                    HTML("&nbsp;"),
                                    actionButton("RemoveFastQbut_R1R2",'Remove file(s)',icon=icon("remove"))
                                  )
              ),
              div(style = "text-align:center;",actionButton("submit", h4(strong("Check and submit")), icon("chevron-circle-right",class="fa-2x"),class="btn-primary",style = "color: #fff"))
330
            ),
svolant's avatar
svolant committed
331
332
333
334
335
336
337
338
            column(width=2,
                   uiOutput("InfoMasque"),
                   uiOutput("InfoMasqueHowTo")
                   )

          )
            
    ),
339

stevenn's avatar
stevenn committed
340
341
342
    tabItem(tabName = "Upload",
            tags$style(type='text/css', ".well { max-width: 20em; }"),
            fluidRow(
Stevenn Volant's avatar
Stevenn Volant committed
343
344
              column(width=3,valueBoxOutput("valueErrorPercent",width=NULL)),
              column(width=3,infoBoxOutput("InfoErrorCounts",width=NULL)),
svolant's avatar
svolant committed
345
346
              column(width=3,infoBoxOutput("InfoErrorTaxo",width=NULL)),
              column(width=3,infoBoxOutput("InfoTreePhylo_box",width=NULL))
Stevenn Volant's avatar
Stevenn Volant committed
347
348
349
350
            ),
            br(),
             fluidRow(
                box(title="Select your file format",width = 3,status = "success", solidHeader = TRUE,collapsible = FALSE,
svolant's avatar
svolant committed
351
352
                  # selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom","Saved project"="fileRData"),selected="fileCounts"),
                  selectInput("FileFormat","",c("Count table & taxonomy (*.csv or *.tsv)"="fileCounts","BIOM file"="fileBiom"),selected="fileCounts"),
svolant's avatar
svolant committed
353
354
355
                  conditionalPanel(condition="input.FileFormat=='fileCounts'",
                                   checkboxInput("NoTaxoFile","No taxonomy table",value=FALSE)
                  )
Stevenn Volant's avatar
Stevenn Volant committed
356
                ),
svolant's avatar
svolant committed
357
                
stevenn's avatar
stevenn committed
358
                conditionalPanel(condition="input.FileFormat=='fileCounts'",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
359
                  box(title="Load the count table",width = 3,height = "260px", status = "primary", solidHeader = TRUE,collapsible = FALSE,
360
                      fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
361
                        column(width=6,radioButtons("TypeTable",h6(strong("Type:")),c("OTU/Gene table"="OTU","MGS table"="MGS"))),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
362
                        column(width=6,selectInput("sepcount", h6(strong("Separator:")),c("Tab" = "\t", "Comma" = ",","Semi-colon" = ";")))
363
                      ),
svolant's avatar
svolant committed
364
365
                      fileInput('fileCounts', h6(strong('Select your file')),width="100%"),
                      tags$script('$( "#fileCounts" ).on( "click", function() { this.value = null; });')
stevenn's avatar
stevenn committed
366
                  ),
svolant's avatar
svolant committed
367
368
369
370
371
372
373
374
375
376
377
                  conditionalPanel(condition="!input.NoTaxoFile",
                    box(title="Load the taxonomy file",width = 3,height = "260px", 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))
                          ),
                          column(width=6,
                                 conditionalPanel(condition="input.TypeTaxo=='Table'",selectInput("septaxo", h6(strong("Separator:")),
                                                      c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";")))
                                 )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
378
                        ),
svolant's avatar
svolant committed
379
380
                        fileInput('fileTaxo', h6(strong('Select your file')),width="100%"),
                        tags$script('$( "#fileTaxo" ).on( "click", function() { this.value = null; });')
svolant's avatar
svolant committed
381
                    )
stevenn's avatar
stevenn committed
382
383
384
385
                  )
                ),
                
                conditionalPanel(condition="input.FileFormat=='fileBiom'",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
386
                                 box(title="Load the BIOM file",width = 3, status = "primary", solidHeader = TRUE,collapsible = FALSE,
svolant's avatar
svolant committed
387
388
                                     fileInput('fileBiom', h5(strong('Select your file')),width="100%"),
                                     tags$script('$( "#fileBiom" ).on( "click", function() { this.value = null; });')
svolant's avatar
svolant committed
389
390
391
392
393
394
395
396
397
398
399
400
401
                                 )
                ),
                
                box(title="Load phylogenetic tree (optional)",width = 3, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
                    fileInput('fileTree', h6(strong('Select your file (tree)')),width="100%"),
                    tags$script('$( "#fileTree" ).on( "click", function() { this.value = null; });')
                ),
                
                fluidRow(column(width=3,
                                uiOutput("InfoCountsFile"),
                                uiOutput("InfoTaxoFile"),
                                uiOutput("InfoBIOM")
                )
stevenn's avatar
stevenn committed
402
                )
svolant's avatar
svolant committed
403
404
                
                
Stevenn Volant's avatar
Stevenn Volant committed
405
             ),
stevenn's avatar
stevenn committed
406
407
408
              column(12,uiOutput("TabBoxData"))

              
Stevenn Volant's avatar
Stevenn Volant committed
409
          
stevenn's avatar
stevenn committed
410
411
    ),
    
stevenn's avatar
stevenn committed
412
413
414
  #### Statistical analysis

    tabItem(tabName = "RunDiff",
stevenn's avatar
stevenn committed
415
            fluidRow(
416
              column(width=3,valueBoxOutput("RowTarget",width=NULL)),
stevenn's avatar
stevenn committed
417
              column(width=3,infoBoxOutput("InfoTaxo",width=NULL)),
418
              column(width=3,infoBoxOutput("InfoDESeq",width=NULL)),
419
              column(width=3,infoBoxOutput("InfoContrast",width=NULL))
Stevenn Volant's avatar
Stevenn Volant committed
420
            ),            
stevenn's avatar
stevenn committed
421
            fluidRow(
stevenn's avatar
stevenn committed
422
423
424
              column(width=5,
                box(title="Experimental design",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = FALSE,
                  fluidRow(
svolant's avatar
svolant committed
425
426
                    column(width=5,fileInput('fileTarget', h6(strong('Select your target file')),width="100%"),
                           tags$script('$( "#fileTarget" ).on( "click", function() { this.value = null; });')
svolant's avatar
svolant committed
427
                           ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
428
429
                    column(width=3,selectInput("septarget", h6(strong("Separator:")), c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";"))),
                    column(width=4,uiOutput("SelectTaxo"))
stevenn's avatar
stevenn committed
430
431
432
                  ),
                  fluidRow( 
                    column(width=6,uiOutput("SelectInterestVar")),
433
434
435
                    column(width=6,uiOutput("SelectInteraction2"))
                  ),
                  fluidRow( 
436
                    column(width=6,uiOutput("RunButton"))
stevenn's avatar
stevenn committed
437
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
438
                ),
439
                fluidRow(uiOutput("InfoModel"),uiOutput("InfoModelHowTo")),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
440
441
                uiOutput("BoxTarget"),
                uiOutput("BoxCountsMerge")
stevenn's avatar
stevenn committed
442
              ),
svolant's avatar
svolant committed
443
              
stevenn's avatar
stevenn committed
444
              column(width=7,
svolant's avatar
svolant committed
445
                  box(title="Options",width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
                    tabBox(title="", id="tabsetOption", width=NULL,
                           tabPanel("Statistical model", 
                                    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,
                                             radioButtons("CooksCutOff",h6(strong("Cooks cut-off")),choices = c("Auto"='Auto',"No cut-off"=Inf,"Value"="val")),
                                             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"))
                                      )
                                      # column(width=3,uiOutput("RefSelect"))
                                    )
                           ),
                           tabPanel("Normalization", 
                                    fluidRow(
                                      column(width=3,
                                             selectizeInput("AccountForNA", h6(strong("Normalization method")),choices = c("Usual"="All", "Remove null counts"="NonNull", "Weighted"="Weighted"),selected = "NonNull")),
                                      column(width=3,
                                             uiOutput("SelectVarNorm")),
                                      column(width=3,
svolant's avatar
svolant committed
484
485
                                             fileInput('fileSizeFactors', h6(strong('Define your own size factors')),width="100%"),
                                             tags$script('$( "#fileSizeFactors" ).on( "click", function() { this.value = null; });')
486
487
488
489
490
491
492
493
494
495
496
497
498
499
                                      ),
                                      column(width=3, selectInput("sepsize", h6(strong("Separator:")), c("Tab" = "\t", "," = "Comma", "Semicolon" = ";"))),
                                      column(width=3,br(),htmlOutput("InfoSizeFactor"))
                                    )
                           ),
                           tabPanel("Filtering",
                                    fluidRow(
                                      tags$div(title="If your count matrix is very sparse, you can add a filter on your data",
                                               column(width=3,checkboxInput("AddFilter","Add a filtering step",value = FALSE))
                                      )
                                    ),
                                    fluidRow(
                                      conditionalPanel(condition="input.AddFilter",
                                              column(width=6, 
500
                                                     plotOutput("Plot_ThSamp"),
501
502
503
                                                     column(width=10,uiOutput("ThSamp"),offset = 1)
                                                     ),
                                              column(width=6,
504
                                                     plotOutput("Plot_ThAb"),
505
506
507
508
509
510
511
512
                                                     column(width=10,uiOutput("ThAb"),offset = 1)
                                                     ),
                                              column(width=12,
                                                     scatterD3Output("Plot_Scatter_Filter")
                                              )
                                      )
                                    )
                           )
svolant's avatar
svolant committed
513
                    )
svolant's avatar
svolant committed
514
515
516
517
518
519
520
521
522
523
524
525
526
                  ),
                  fluidRow(
                    column(width=8,
                            uiOutput("contrastBox"),
                           uiOutput("contrastBoxAdvanced")
                           ),
                    column(width=4,
                      
                           uiOutput("contrastDefined"),
                           uiOutput("InfoContrast_box")
                      )
                  )
                  
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
527
              )
stevenn's avatar
stevenn committed
528
            )
svolant's avatar
svolant committed
529
530
              
            
stevenn's avatar
stevenn committed
531
    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
532
    tabItem(tabName = "DiagPlotTab",
stevenn's avatar
stevenn committed
533
            fluidRow(
stevenn's avatar
stevenn committed
534
              column(width=9,
svolant's avatar
svolant committed
535
536
537
538
539
                     tags$head(tags$style(HTML(spincss))),
                     div(id = "plot-container",
                         tags$img(src = "gears.gif",id ="loading-spinner"),
                         plotOutput("PlotDiag",height="100%")
                     ),
Stevenn Volant's avatar
Stevenn Volant committed
540
                br(),
541
                conditionalPanel(condition="input.DiagPlot=='SfactorsVStot'",
stevenn's avatar
stevenn committed
542
                  box(title = "Size factors",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
543
                    DT::dataTableOutput("SizeFactTable"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
544
545
546
547
548
                    fluidRow( 
                      column(width=3,downloadButton('ExportSizeFactor', 'Export table')),
                      column(width=3,selectInput("sepsizef", h6(strong("Separator:")), c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";")))
                    ),
                    tags$style(type='text/css', "#ExportSizeFactor { margin-top: 37px;}")
stevenn's avatar
stevenn committed
549
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
550
                ),
svolant's avatar
svolant committed
551
                  fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
552
553
                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
554
                                    plotOutput("PlotEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
555
556
                                 )
                ),
svolant's avatar
svolant committed
557
                
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
558
559
                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
560
                                     plotOutput("PlotpcoaEigen",height="100%")
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
561
                                 )
svolant's avatar
svolant committed
562
                ),
svolant's avatar
svolant committed
563
564
565
566
567
                conditionalPanel(condition="input.DiagPlot=='nmdsPlot'",
                                 box(title = "Stress plot",  width = 6, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
                                     plotOutput("PlotnmdsStress",height="100%")
                                 )
                ),
svolant's avatar
svolant committed
568
569
                conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='nmdsPlot'",
                                 uiOutput("ResPermaTestBox")
stevenn's avatar
stevenn committed
570
                )
svolant's avatar
svolant committed
571
                  )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
572
                
stevenn's avatar
stevenn committed
573
574
              ),
              column(width=3,
575
576
                box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
                  selectInput("DiagPlot","",c("Total barplot"="barplotTot","Nul barplot"="barplotNul",
577
                                              "Maj. taxonomy"="MajTax","Boxplots" = "boxplotNorm", "Density"="densityPlot", "Dispersion" = "DispPlot",
svolant's avatar
svolant committed
578
                                              "Size factors VS total"="SfactorsVStot", "PCA"="pcaPlot", "PCoA"="pcoaPlot","NMDS"="nmdsPlot","Clustering" = "clustPlot"))
579
                    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
580
                box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
581
                    conditionalPanel(condition="input.DiagPlot!='clustPlot' && input.DiagPlot!='pcaPlot' && input.DiagPlot!='SfactorsVStot' && input.DiagPlot!='DispPlot'",
582
                                     radioButtons("CountsType","Counts:",c("Normalized"="Normalized","Raw"="Raw"),inline = TRUE)
583
                                     ),
584
585
586
                    conditionalPanel(condition="input.DiagPlot=='boxplotNorm'",
                                    checkboxInput("RemoveNullValue","Remove 0",value = TRUE)
                                    ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
587
                    conditionalPanel(condition="input.DiagPlot!='Sfactors' && input.DiagPlot!='SfactorsVStot' ",uiOutput("VarIntDiag")),
svolant's avatar
svolant committed
588
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='pcaPlot' || input.DiagPlot=='nmdsPlot'",
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
589
                                     h5(strong("Select the modalities")),
svolant's avatar
svolant committed
590
591
592
593
594
595
                                     uiOutput("ModMat"),
                                     fluidRow(
                                       column(width=5,uiOutput("PC1_sel")),
                                       column(width=2,br(),br(),p("VS")),
                                       column(width=5,uiOutput("PC2_sel"))
                                     )
596
                                    ),
svolant's avatar
svolant committed
597
                    conditionalPanel(condition="input.DiagPlot=='pcoaPlot' || input.DiagPlot=='nmdsPlot' || input.DiagPlot=='SERE' || input.DiagPlot=='clustPlot' ",
svolant's avatar
svolant committed
598
599
600
601
602
603
604
                                      uiOutput("DistList")
                                    ),
                    conditionalPanel(condition="input.DistClust=='Unifrac' && (input.DiagPlot=='pcoaPlot' || input.DiagPlot=='nmdsPlot'  || input.DiagPlot=='clustPlot')",
                      column(width=12,
                           selectInput("DistClustUnifrac","Which unifrac distance ?",c("Weighted UniFrac"="WU", "Unweighted UniFrac"="UWU", "Variance adjusted weighted UniFrac"="VAWU"))
                      )
                    )
Stevenn Volant's avatar
Stevenn Volant committed
605
                    
svolant's avatar
svolant committed
606

stevenn's avatar
stevenn committed
607
608
609
610
611
#                 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)) 
               ),
svolant's avatar
svolant committed
612

stevenn's avatar
stevenn committed
613
614
                box(
                  title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
615
616
617
618
#                     conditionalPanel(condition="input.DiagPlot=='Sfactors'",
#                                      h6(strong("Layout")),
#                                      numericInput("NbcolSfactors", h6("Columns"),min=1,value = NA)
#                     ),
Stevenn Volant's avatar
Stevenn Volant committed
619
                  sliderInput("heightDiag", "Height",min=100,max=1500,value = 500,step =10),
620
621
622
                  checkboxInput("modifwidthDiag","Set width",FALSE),
                  conditionalPanel(condition="input.modifwidthDiag",
                  sliderInput("widthDiag", "Width",min=100,max=2500,value = 800,step =10)),
Stevenn Volant's avatar
Stevenn Volant committed
623

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
624
625
626
627
628
                  conditionalPanel(condition="input.DiagPlot=='clustPlot'",
                                   h6(strong("Layout")),
                                   selectInput("typeHculst", h6("Type"),c("Horizontal"="hori","Fan"="fan")),
                                   checkboxInput("colorHC","Add color",value=TRUE)
                  ),
svolant's avatar
svolant committed
629

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
630
631
632
633
634
635
636
                  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)
                                   
                  ),
svolant's avatar
svolant committed
637

Stevenn Volant's avatar
Stevenn Volant committed
638
639
640
641
642
643
644
                  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)),
svolant's avatar
svolant committed
645
                    conditionalPanel(condition="input.DiagPlot=='SfactorsVStot' || input.DiagPlot=='pcaPlot' || input.DiagPlot=='pcoaPlot' || input.DiagPlot=='nmdsPlot' ",column(width=6,sliderInput("cexLabelDiag", h6("Points"),min=0,max=5,value = 1,step =0.1)))
Stevenn Volant's avatar
Stevenn Volant committed
646
647
                  )

Amine  GHOZLANE's avatar
Amine GHOZLANE committed
648
649
#                   sliderInput("widthDiag", "width",min=100,max=1500,value = 1000,step =10)
                 
stevenn's avatar
stevenn committed
650

stevenn's avatar
stevenn committed
651
652
653
654
655
656
657
658
659
660
661
662
663
664
              ),
              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
665
666
667
              )
            )
        )
stevenn's avatar
stevenn committed
668
669
670
    ),
    tabItem(tabName = "TableDiff",
            fluidRow(
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
671
672
673
674
675
              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")
676
677
                     ),
                     box(title = "Export",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
678
679
680
681
                         fluidRow(
                           column(width=8,selectInput("WhichExportTable", "Select the table to export",c("Significant"="Significant","Complete"="Complete","Up"="Up","Down"="Down"))),
                           column(width=4,selectInput("sepexpdiff", "Separator:", c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";")))
                         ),
svolant's avatar
svolant committed
682
                         uiOutput("ExportTableButton")
683
                     )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
684
            )
Stevenn Volant's avatar
Stevenn Volant committed
685
            ) 
stevenn's avatar
stevenn committed
686
687
688
689
    ),
  
  #### Data Viz
  
690
  tabItem(tabName = "GlobVisu",
stevenn's avatar
stevenn committed
691
          fluidRow(
692
            column(width=9,
svolant's avatar
svolant committed
693
694
695
696
697
                   tags$head(tags$style(HTML(spincss))),
                   div(id = "plot-container",
                       conditionalPanel(condition="input.PlotVisuSelect=='Boxplot' || input.PlotVisuSelect=='Diversity' || input.PlotVisuSelect=='Rarefaction'",   
                                          tags$img(src = "gears.gif",id ="loading-spinner")
                                        ),
svolant's avatar
svolant committed
698
                       uiOutput("plotVisu"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
699
700
                       #conditionalPanel(condition="input.PlotVisuSelect!='Krona'",),
                       #conditionalPanel(condition="input.PlotVisuSelect=='Krona'",tags$script(uiOutput("plotVisu"))),
svolant's avatar
svolant committed
701
702
703
                       conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot' && !input.AddRegScatter",
                                        p(actionButton("scatterD3-reset-zoom", HTML ("<span class='glyphicon glyphicon-search' aria-hidden='true'></span> Reset Zoom")),Align="right")
                       )
svolant's avatar
svolant committed
704
705
                   ),
                   
svolant's avatar
svolant committed
706
                   
707
                   ### Regression and correlation outputs for the scatter plot
svolant's avatar
svolant committed
708
                   conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot' && input.AddRegScatter", 
svolant's avatar
svolant committed
709
710
711
712
                                    fluidRow(
                                      column(width=6,
                                      br(),
                                      box(title = "Regression coefficients",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
713
                                          DT::dataTableOutput("lmRegScatter")
svolant's avatar
svolant committed
714
                                      )
svolant's avatar
svolant committed
715
716
                                    ),
                                    column(width=6,br(),htmlOutput("lmEquation"))
svolant's avatar
svolant committed
717
                                    )
718
719
720
721
722
                   ),
                   conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot'",
                                    useShinyjs(),
                                    br(),
                                    box(title = "Correlation table",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
723
                                        DT::dataTableOutput("CorTable")
724
725
726
727
728
729
                                    )
                   ),
                   
                   ## Values of the diversities
                   conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
                                    br(),
svolant's avatar
svolant committed
730
                      box(title = "Diversity values",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
731
                          DT::dataTableOutput("Diversitytable"),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
732
733
734
735
736
                          fluidRow(
                            column(width=3,downloadButton('ExportDiversitytable', 'Export table')),
                            column(width=3,selectInput("sepdiversity", "Separator:", c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";")))
                          ),
                          tags$style(type='text/css', "#ExportDiversitytable { margin-top: 37px;}")
737
738
                      )
                   ) 
svolant's avatar
svolant committed
739
740
                                    
                   ),
741
            
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
742
            column(width=3,
743
              box(title = "Select your plot",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = FALSE,collapsed= FALSE,
744
                  selectizeInput("PlotVisuSelect","",c("Barplot"="Barplot","Heatmap"="Heatmap","Boxplot"="Boxplot","Tree"="Tree","Scatterplot"="Scatterplot","Diversity"="Diversity","Rarefaction"="Rarefaction","Krona"="Krona"),selected = "Barplot")
745
              ),
746
            
747

748
749
750
751
752
              ########################################################################
              ###
              ###               Options Visualization
              ###
              ########################################################################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
753
              box(title = "Options",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= FALSE,
754
755
756
                  conditionalPanel(condition="input.PlotVisuSelect",
                                   radioButtons("NormOrRaw",label = h5(strong("Type of counts")), c("Normalized" = "norm", "Raw" = "raw"),inline=TRUE)
                  ),
757
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Scatterplot' && input.PlotVisuSelect!='Tree'",
svolant's avatar
svolant committed
758
                                   uiOutput("VarIntVisu"),
759
760
                                   h5(strong("Select the modalities")),
                                   uiOutput("ModVisu")
761
                  ),
762
763
764
                  # conditionalPanel(condition="input.PlotVisuSelect=='Tree'",
                  #                   uiOutput("VarIntVisuTree")),
                  conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot'",
svolant's avatar
svolant committed
765
                                   uiOutput("VarIntVisuScatter"),
766
767
                                   radioButtons("TransDataScatter","Data transformation",c("Log2 +1" = "log2","None" = "none"),inline=TRUE),
                                   hr(),
768
                                   radioButtons("CorMeth","Correlation method",c("Pearson" = "pearson", "Spearman" = "spearman"),inline=TRUE),
svolant's avatar
svolant committed
769
770
                                   checkboxInput("AddRegScatter","Add regression line",FALSE)
                  ),                 
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
771
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot' && input.PlotVisuSelect!='Krona'",
svolant's avatar
svolant committed
772
                                   radioButtons("SelectSpecifTaxo","Select the features",c("Most abundant"="Most","All"="All", "Differential features" = "Diff", "Non differential features" = "NoDiff"))
773
                  ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
774
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot' && (input.SelectSpecifTaxo=='Diff' || input.SelectSpecifTaxo=='NoDiff') && input.PlotVisuSelect!='Krona' ",
775
776
                                   selectizeInput("ContrastList_table_Visu","",choices = "", multiple = TRUE),
                                   radioButtons("UnionInterContrasts","Union or intersection ?",c("Union"="Union","Intersection"="Inter"),inline = TRUE)
777
                  ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
778
                  conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Diversity' && input.PlotVisuSelect!='Scatterplot' && input.PlotVisuSelect!='Krona'",
779
780
781
782
783
784
785
                                   uiOutput("TaxoToPlotVisu")
                  ),

                ##################
                ## BARPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Barplot'",
786
                                 hr(),
787
788
789
790
791
792
793
794
                                 selectizeInput(inputId = "CountsOrProp",label = h6(strong("Type of data")),choices = c("Proportions" = "prop", "Counts" = "counts"),selected = "prop")
                ),
                
                
                ##################
                ## HEATMAP
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Heatmap'",
795
796
797
                                 selectizeInput(inputId = "scaleHeatmap",label = h5(strong("Scale:")),choices = c("None" = "none", "Rows" = "row", "Column" = "col"),selected = "none"),
                                 radioButtons("SortHeatRow","Row Clustering:", c("Yes" ="Yes","No" = "No"),inline=TRUE),
                                 radioButtons("SortHeatColumn","Column Clustering:", c("Yes" ="Yes","No" = "No"), inline=TRUE)
798
799
800
801
802
803
804
                                 
                ),
                
                ##################
                ## BOXPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Boxplot'",
805
                                 hr(),
806
807
808
809
810
811
812
                                 selectizeInput("typeDataBox",h6(strong("Type of data")),c("Log2"="Log2","Relative"="Relative"))
                ),
                
                ##################
                ## DIVERSITY
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
813
814
815
816
                                 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")
817
                )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
818
              ),
819
820


821
822
823
824
825
              ########################################################################
              ###
              ###               Appearance Visualization
              ###
              ########################################################################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
826
              box(title = "Appearance",  width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed= TRUE,
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
827
                sliderInput("heightVisu", h6(strong("Height")),min=100,max=4000,value = 800),
828
829
830
831
832
833
834
835
836
                checkboxInput("modifwidthVisu","Set width",value=FALSE),
                conditionalPanel(condition="input.modifwidthVisu",
                sliderInput("widthVisu", h6(strong("Width")),min=100,max=4000,value = 800)),
                ##################
                ## BARPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Barplot'",
                                 sliderInput("rotateXLabel", h6(strong("Rotate X labels (Only vertical orientation)")),min=-90, max=90,value = 0, step = 5)  
                ),
837
838
839
840
                ##################
                ## BOXPLOT
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Boxplot'",
841
                                 uiOutput("ColBoxplot"),
Stevenn Volant's avatar
Stevenn Volant committed
842
                                 radioButtons("ScaleBoxplot","Scales",c("Fixed"="fixed","Free"="free"),inline=TRUE),
843
844
845
846
847
848
                                 checkboxInput("CheckAddPointsBox","Add points",value=TRUE)
                ),
                ##################
                ## DIVERSITY
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Diversity'",
849
850
                                 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)
851
852
853
854
                ),
                ##################
                ## HEATMAP
                ##################
855
                conditionalPanel(condition="input.PlotVisuSelect=='Heatmap'",
Stevenn Volant's avatar
Stevenn Volant committed
856
                                 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")
857
858
859
860
861
862
863
864
865
866
867
868
                ),
                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))
                                 )
869
                ),
svolant's avatar
svolant committed
870
871
872
873
874
875
876
877
878
879
                
                ##################
                ## Scatterplot
                ##################
                conditionalPanel(condition="input.PlotVisuSelect=='Scatterplot'",
                                 fluidRow(
                                   column(width=12,sliderInput("SizeLabelScatter", h6("Label size"),min=0,max=50,value = 10,step = 1))
                                  )
                ),
                
880
881
882
                ##################
                ## ALL
                ##################
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
883
                conditionalPanel(condition="input.PlotVisuSelect!='Rarefaction' && input.PlotVisuSelect!='Scatterplot' && input.PlotVisuSelect!='Krona' && input.PlotVisuSelect!='Phylogeny'",
884
885
                                 radioButtons(inputId = "SensPlotVisu",label = h6(strong("Orientation")),choices = c("Vertical" = "Vertical", "Horizontal" = "Horizontal"),selected = "Vertical",inline = TRUE)
                )
Stevenn Volant's avatar
Stevenn Volant committed
886
              ),
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
              conditionalPanel(condition="input.PlotVisuSelect!='Krona' && input.PlotVisuSelect!='Phylogeny'",
                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")
                )
902
              )
Amine  GHOZLANE's avatar
Amine GHOZLANE committed
903
904
905
906
            )
          )
  ),

907
908
909
910
911
  tabItem(tabName = "CompPlot",
          fluidRow(
            column(width=9,
                   uiOutput("plotVisuComp"),
                   conditionalPanel(condition="input.PlotVisuSelectComp=='Venn'",
912
                                    DT::dataTableOutput("DataVenn")
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
                   )
            ),
            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),
937
938
939
                       checkboxInput("modifwidthComp","Set width",FALSE),
                       conditionalPanel(condition="input.modifwidthComp",
                                        sliderInput("widthComp", "Width",min=100,max=2500,value = 800,step =10)),
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
                       ##################
                       ## 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
978
979
  #### Krona plot
  tabItem(tabName = "Krona",