BioNetStat: Biological Network Analysis

# ------------------------------------------------------------------------------
# BioNetStat User Interface (UI) definition
# ------------------------------------------------------------------------------
library(shiny)
# library(shinyBS)
# library(BioNetStat)
# Define UI for application
shinyUI(fluidPage(theme = "bootstrap.css",

#   # Application title --------------------------------------------------------
  headerPanel(
    p(img(src="images/figuraBNS.png"), align="center"),
    windowTitle="BioNetStat"
  ),

  # Sidebar to load data and set application parameters ----------------------
  sidebarPanel(
    # Input files
    h3("1. Load data"),
    wellPanel(
      h4(strong("Variables values data")),
      fileInput("expr", h5(paste("Please, select the text file (*.csv) containing the variables values data"),
                          img(src="images/info.png", title="Choose a file containing the table with the variables in the colums and the samples in the rows. The conditions of measure rows have to be indicated by a factor column")),
                accept=c("Comma-Seperated Values", "text/csv", ".csv",".txt"),placeholder = "Select a variable values file")
    ),
    uiOutput("classes"),
    uiOutput("factors"),
    wellPanel(
      h4(strong("Variable set database")),
      fileInput("geneSets",
                h5(paste("Load the Set of variables file (*.txt)",
                      "describing the variables sets"),img(src="images/info.png", title="Choose a file containing the groups of variables. The format of the file that has to be inserted is explained in help section.")),
                accept=c('.gmt',".txt"),placeholder = "Select a variables groups file")
    ),
    # Parameters
    h3("2. Set parameters"),
    wellPanel(
      h4(strong("Variable sets size range")),
      h5("Enter the minimum and maximum variable set sizes."),
      uiOutput("minSize"),
      uiOutput("maxSize"),
      uiOutput("geneSetsCount")
    ),
    wellPanel(
      h3("Network construction"),
      h4(strong("a. Method for network inference")),
      uiOutput("correlationMeasure"),
      h4(strong("b. Network type")),
      radioButtons(
        "networkType",
        h5("Select what network type will be compared"),
        c("Weighted"="weighted", "Unweighted"="unweighted")
      ),
      h4(strong("c. Set the statistic used\n as link formation threshold")),
      conditionalPanel(
        "input.networkType=='weighted'",
        selectInput(
        "thrMeasure",
        h5("Association measure"),
        c("Absolute correlation"="correlation", "1 - p-value"="pvalue",
          "1 - q-value"="qvalue","No threshold"="none")
        )
      ),
      conditionalPanel(
        "input.networkType=='unweighted'",
        selectInput(
          "thrMeasure",
          h5("Association measure"),
          c("Absolute correlation"="correlation", "1 - p-value"="pvalue",
            "1 - q-value"="qvalue")
        )
      ),
      uiOutput("linkFormation"),
      conditionalPanel(
        "input.networkType=='weighted'",
        radioButtons(
          "edgeWeight",
          h4(strong("d. Set the criterion for network edges weights:")),
          c("Absolute correlation"="correlation", "1 - p-value"="pvalue",
            "1 - q-value"="qvalue")
        )
      )
    ),
    wellPanel(
      h4(strong("Method for networks comparison")),
      uiOutput("networkTest"),
      uiOutput("networkTestDescription"),
      uiOutput("networkTestOptions")
    ),
    wellPanel(
      h4(strong("Permutation test settings")),
      numericInput("numPermutations",
                   "Enter the number of label permutations:",
                   1000, min=0),
      numericInput("seed",
                   "Enter a seed to generate random permutations:", 0)
    ),
    h3("3. Run differential network analysis"),
    wellPanel(
      actionButton("start", "Start analysis", class = "btn-primary")
    )
    ),
  # Main panel ---------------------------------------------------------------
  mainPanel(
    h3("Reports"),

    # Tabset
    tabsetPanel(
      id="tabSelected",
      # Data tab
      tabPanel(
        h5("Loaded data"),
        h5("Variable values data"),
        uiOutput("expr"),
        h5("Sample labels"),
        uiOutput("labels"),
        h5("Variable sets collection"),
        uiOutput("geneSets"),
        value = "Loaded data",
        dataTableOutput("table")
      ),
      # Results tab
      tabPanel(
        h5("Analysis results"),
        # bsAlert(inputId = "resultsWarning"),
        bsAlert(anchorId =  "resultsWarning"),
        # progressInit(),
        uiOutput("appMessages"),
        uiOutput("isCompleted"),
        wellPanel(
          uiOutput("resultsType"),
          uiOutput("downloadResultsButton")
        ),
        DT::dataTableOutput("results"),# 'datatables'
        # chartOutput('results', 'datatables'),
        value = "Analysis results"
      ),
      # Further analysis tab
      tabPanel(
        h5("Further analyses"),
        wellPanel(
          h5("Variable set selection"),
          div(
            class="row-fluid",
            div(class="span6", uiOutput("filterGeneSets"),
                uiOutput("geneSetThreshold")),
            div(class="span6", uiOutput("selectGeneSet"))
          ),
          uiOutput("geneSetInfo")
        ),

        br(),
        uiOutput("selectedGeneSet"),
        tabsetPanel(
          id="FurtherTabSelected",
          tabPanel(
            "Nodes differential analysis",
            wellPanel(
              h4("Nodes Test"),
              uiOutput("vertexFunction"),
              h4("Run differential node analysis"),
              # actionButton("startVertex", "Start analysis"),
              # bsAlert(inputId = "vertexResultsWarning"),
              uiOutput("vertexScoresType"),
              uiOutput("downloadVertexAnalysisButton")
            ),
            br(),
            DT::dataTableOutput("vertexAnalysisTable"),
            bsCollapsePanel(
              "KEGG pathway visualization",
              h4(strong("KEGG codes")),
                fileInput("keggCodes", h5(tagList("Please, select the codes table (*.csv) containing the variables names and coresponding Kegg code. The KEGG codes can be find in ", a("KEGG website.", href="http://www.kegg.jp/",target="_blank"))),
                          accept=c("Comma-Seperated Values", "text/csv", ".csv"),placeholder = "Select a file"),
              textOutput("codeFile"),
              tags$head(tags$style("#codeFile{color: red}")),
              div(
                class="span4",
                h4(strong("Colors selection")),
                uiOutput("exprKeegMapColors"),
                radioButtons(
                  "selectingDataType",
                  "Select a what kind of data you are analysing:",
                  c("Genes or/and Proteins"="gene", "Metabolite"="cpd"))
              ),
              selectInput(
                "thresholdSelected",
                h4(strong("Association measure")),
                c("p-value"="pvalue",
                  "q-value"="qvalue","Test statistics"="statistic")
              ),
              uiOutput("thrValue"),
              h4(strong("Specie code")),
              textInput("speciesID", label = h5("Write the code of the species that you want to analyze. The species codes can be find in ", a("KEGG website.", href="http://www.kegg.jp/kegg/pathway.html",target="_blank")), value = "code"),
              h4(strong("Path code")),
              textInput("pathID", label = h5("Write the code of the pathway that you want to analyze. The pathways codes can be find in ", a("KEGG website.", href="http://www.kegg.jp/kegg/catalog/org_list.html",target="_blank")), value = "code"),
              checkboxInput("keggNative", label = "Kegg Native plot", value = TRUE),
              downloadButton("downloadKeggMap","Save the Kegg Map"),
              h5("The download of kegg map may take a while.")
            )
          ),
          ## NETWORK VISUALIZATION
          tabPanel(
            "Network visualization plots",
            div(
              class="span4",
              h3("Classes selection"),
              uiOutput("factorsToNetViz1"),
              uiOutput("factorsToNetViz2")
            ),
            br(),
          bsCollapsePanel(
            "Plot settings",
            div(
              class="row-fluid",
              div(
                class="span4",
                h4(strong("Colors selection")),
                uiOutput("heatmapColors")
              ),
              div(
                class="span4",
                h4(strong("Plot format")),
                radioButtons(
                  "networkPlotFormat",
                  "Select a format to save the plots:",
                  c("PDF","PNG", "JPG"))
              ),
              div(
                class="span4",
                h4(strong("Plot dimensions")),
                uiOutput("networkPlotDimensions")
              )
            )
          ),
          bsCollapsePanel(
            "Network visualization",
            conditionalPanel(
              "input.edgeWeight=='correlation'",
              checkboxInput("signedCorrelation",
                            "Show negative correlations")
            ),
            br(),
            div(class="row-fluid",
                div(class="span6", plotOutput("heatmapClass1"),
                    uiOutput("downloadNetworkPlot1Button")),
                div(class="span6", plotOutput("heatmapClass2"),
                    uiOutput("downloadNetworkPlot2Button"))),
            br(),
            wellPanel(
              h4(strong("Association between two variable values")),
              uiOutput("selectGenes"),

              dataTableOutput("corr")
            )
          ),
          bsCollapsePanel(
            "Differences between set properties",
            wellPanel(
              h4(strong("Node set network topological properties")),
              uiOutput("networkScore"),
              uiOutput("networkScoreOptions"),
              uiOutput("networkScoresComparison")
            )
          ),
          bsCollapsePanel(
            "Differences between networks",
            uiOutput("heatmapDiffOptions"),
            br(),
            bsCollapsePanel(
              "Matrix of differences",
              plotOutput("heatmapDiff", width="50%"),
              uiOutput("downloadNetworkDiffPlotButton")),
            bsCollapsePanel(
              "List of nodes association degrees",
              wellPanel(
                uiOutput("absDiffType"),
                uiOutput("downloadAbsDiffButton")
              ),
              br(),
              DT::dataTableOutput("corAbsDiff")#, "datatables")
              # chartOutput("corAbsDiff")#, "datatables")
            )
          ),
          bsCollapsePanel(
            "List of nodes association to be read by S.I.T.",
            wellPanel(
              uiOutput("sitTableType"),
              uiOutput("downloadsitTableButton")
            ),
            br(),
            DT::dataTableOutput("sitTable")#, "datatables")
            # chartOutput("corAbsDiff")#, "datatables")
          )
          ),
          # tabPanel(
          #   "Node scores",
          #   wellPanel(
          #     h5("Node scores"),
          #     uiOutput("geneScore"),
          #     uiOutput("geneScoresType"),
          #     uiOutput("downloadGeneScoresButton")
          #   ),
          #   br(),
          #   dataTableOutput("geneScoresComparison")
          #   # chartOutput("geneScoresComparison", "datatables")
          # ),
          tabPanel(
            "Variable values analysis",
            bsCollapsePanel(
              "Variable values heatmap",
              wellPanel(
                div(
                  class="row-fluid",
                  div(class="span4",
                      h4(strong("Colors selection")),
                      uiOutput("exprHeatmapColors"),
                      h4(strong("Heatmap clustering options")),
                      uiOutput("exprHeatmapClustering")),
                  div(
                    class="span4",
                    h4(strong("Plot format")),
                    radioButtons(
                      "exprHeatmapFormat",
                      "Select a format to save the plots:",
                      c("PDF","PNG", "JPG"))
                  ),
                  div(class="span4",
                      h4(strong("Plot dimensions")),
                      uiOutput("exprHeatmapDimensions"),
                      uiOutput(paste("downloadExpr",
                                     "HeatmapButton",
                                     sep="")))
                )
              ),
              plotOutput("exprHeatmap", width="100%")
            ),
            bsCollapsePanel(
              "KEGG pathway visualization",
              h4(strong("KEGG codes")),
              fileInput("keggCodes2", h5(tagList("Please, select the codes table (*.csv) containing the variables names and coresponding Kegg code. The KEGG codes can be find in ", a("KEGG website.", href="http://www.kegg.jp/",target="_blank"))),
                        accept=c("Comma-Seperated Values", "text/csv", ".csv"),placeholder = "Select a file"),
              textOutput("codeFile2"),
              tags$head(tags$style("#codeFile2{color: red}")),#;
                                 # font-size: 20px;
                                 # font-style: italic;
              div(
                class="span4",
                radioButtons(
                  "selectingDataType2",
                  "Select a what kind of data you are analysing:",
                  c("Genes or/and Proteins"="gene", "Metabolite"="cpd"))
              ),
              selectInput(
                "thresholdSelected2",
                h4(strong("Association measure")),
                c("p-value"="pvalue",
                  "q-value"="qvalue","Test statistics"="statistic")
              ),
              uiOutput("thrValue2"),
              selectInput(
                "funSelected",
                h4(strong("Select an aggregation function")),
                c("Mean"="mean",
                  "Median"="median","Maximum"="max","Minimum"="min")
              ),
              h4(strong("Specie code")),
              textInput("speciesID2", label = h5("Write the code of the species that you want to analyze. The species codes can be find in ", a("KEGG website.", href="http://www.kegg.jp/kegg/pathway.html",target="_blank")), value = "code"),
              h4(strong("Path code")),
              textInput("pathID2", label = h5("Write the code of the pathway that you want to analyze. The pathways codes can be find in ", a("KEGG website.", href="http://www.kegg.jp/kegg/catalog/org_list.html",target="_blank")), value = "code"),
              checkboxInput("keggNative2", label = "Kegg Native plot", value = TRUE),
              downloadButton("downloadKeggExprMap","Save the Kegg Map")
            ),
            bsCollapsePanel(
              "Tests for differential expression",
              wellPanel(
                uiOutput("diffExprTestsType"),
                uiOutput("downloadDiffExprTestsButton")
              ),
              br(),
              DT::dataTableOutput("diffExprTests")
              # chartOutput("diffExprTests", "datatables")
            ),
            bsCollapsePanel(
              "Variable value boxplot",
              wellPanel(
                h4(strong("Variable selection")),
                uiOutput("selectGene")
              ),
              wellPanel(
                div(class="row-fluid",
                    div(class="span6",
                        h4(strong("Plot format")),
                        radioButtons(
                          "exprBoxplotFormat",
                          "Select a format to save the plots:",
                          c("PDF","PNG", "JPG"))),
                    div(class="span6",
                        h4(strong("Plot dimensions")),
                        uiOutput("exprBoxplotDimensions"),
                        uiOutput("downloadExprBoxplotButton"))),
                plotOutput("exprBoxplot", width="100%")
              )
            )
          )
        ),
        value = "Further analyses"


      ),
      # Help tab
      tabPanel(
        h5("Help"),
        bsCollapse(
          multiple=TRUE,
          id="help",
          bsCollapsePanel(
            "1. Loading the dataset",
            includeHTML("help/helpData.html")#,
            # id="helpData"
          ),
          bsCollapsePanel(
            "2. Setting parameters and running the analysis",
            includeHTML("help/helpParameters.html")#,
            # id="helpParameters"
          ),
          bsCollapsePanel(
            "3. Interpreting the results",
            includeHTML("help/helpResults.html")#,
            # id="helpResults"
          )#,
          # bsCollapsePanel(
          #   "4. Further Analyses",
          #   includeHTML("help/helpFurtherAnalyses.html"),
          #   id="helpFurtherAnalyses"
          # ),
          # bsCollapsePanel(
          #   "5. Running BNS from the command-line interface",
          #   includeHTML("help/helpCommandLine.html"),
          #   id="helpCommandLine"
          # ),
          # bsCollapsePanel(
          #   "6. References",
          #   includeHTML("help/helpReferences.html"),
          #   id="helpReferences"
          # )
        ),
        value = "Help"
      ),
      # About tab
      tabPanel(h5("About"), includeHTML("about.html"), value="About")
      ))
))