inst/biblioverApp/ui.R

In biblioverlap: Document-Level Matching Between Bibliographic Datasets

################################### DEFINING UI COMPONENTS #######################################################

custom_styles <-
  tags$style(
    HTML(".custom_title { color: darkcyan; font-family: Arial, sans-serif; text-align: center; font-size: 18px; font-weight: bold; }"),
    HTML(".custom_button { background-color: green; color: white; margin-top: 10px; margin-bottom: 10px }"),
    HTML(".plot_container {
      width: 100%; /* Set the width of the div as needed */
      overflow-x: auto; /* Add a vertical scrollbar if content overflows horizontally */
      border: 2px solid rgba(0, 0, 0, 0.3); border-radius: 2px;
    }"),
    HTML(".justified_text { text-align: justify; }")
  )

favicon <- tags$head(
  tags$link(rel = "icon", href = "biblioverlap_sticker.png") #Setting tab favicon
)


input_data_panel_title <-
  tagList(
    tags$div("Input data options", class = "custom_title"),
    tags$hr()
  )

column_names_ui <-
  tagList(
    tags$b('Column names'),
    tabsetPanel(
      id = "colnames",
      tabPanel("DI",
               textInput("di", "DOI / unique identifier", value = 'DOI')
      ),
      tabPanel("TI",
               textInput('ti', 'Document title', value = 'Title')
      ),
      tabPanel("SO",
               textInput('so', 'Document Source', value = 'Source Title')
      ),

      tabPanel("AU",
               textInput('au', 'Author(s)', value = 'Author/s')
      ),

      tabPanel("PY",
               textInput('py', 'Publication Year', 'Publication Year')
      )
    )
  )


score_matching_params_ui <-
  tagList(
    fluidRow(
      column(6, numericInput('ti_penalty', 'ti_penalty',
                             min = 0, step = 0.1,
                             value = 0.1)),
      column(6, numericInput('ti_max', 'ti_max',
                             min = 0, step = 0.1,
                             value = 0.6))
    ),
    fluidRow(
      column(6, numericInput('so_penalty', 'so_penalty',
                             min = 0, step = 0.1,
                             value = 0.1)),
      column(6, numericInput('so_max', 'so_max',
                             min = 0, step = 0.1,
                             value = 0.3))
    ),
    fluidRow(
      column(6, numericInput('au_penalty', 'au_penalty',
                             min = 0, step = 0.1,
                             value = 0.1)),
      column(6, numericInput('au_max', 'au_max',
                             min = 0, step = 0.1,
                             value = 0.3))
    ),
    fluidRow(
      column(6, numericInput('py_max', 'py_max',
                             min = 0, step = 0.1,
                             value = 0.3)),
      column(6, numericInput('score_cutoff', 'score_cutoff',
                             min = 0, step = 0.1,
                             value = 1))
    )
  )

score_matching_options_ui <-
  tagList(
    tags$strong('Score matching'),
    tags$br(),
    actionButton("change_score_params", "Change parameters", class = 'custom_button'),
    conditionalPanel(
      condition = "input.change_score_params % 2 == 1",
      score_matching_params_ui
    )
  )



n_threads_ui <- sliderInput('n_threads', 'Number of threads',
                            min = 1,
                            max = parallel::detectCores(),
                            value = 1, step = 1
)

n_sets_ui <-
  tagList(
    sliderInput('n_sets', "Number of bibliographical datasets",
                min = 2, max = 7,
                value = 2, step = 1),
    uiOutput("dataset_input_fields")
  )


results_data <-  tabPanel("Data",
                          downloadButton("download_data", "Download Data", class = 'custom_button'),
                          DT::dataTableOutput('full_table')
)


results_summary_table <- tabPanel("Summary",
                                  downloadButton("download_summary_table", "Download Summary Table", class = 'custom_button'),
                                  tableOutput('summary_table')
)

plot_panel_title <-
  tagList(
    tags$div("General plot options", class = "custom_title"),
    tags$hr()
  )


plot_settings <- tagList(
  sliderInput('plot_width', 'Plot Width',
              min = 200, max = 2560,
              value = 640, step = 10
  ),
  tags$br(),
  sliderInput('plot_height', 'Plot Height',
              min = 200, max = 1440,
              value = 480, step = 10
  )
)

results_summary_plot <- tabPanel("Summary",
                                 actionButton("modify_summary", "Modify plot", class = 'custom_button'),
                                 conditionalPanel(
                                   condition = "input.modify_summary % 2 == 1",
                                   fluidRow(
                                     column(2, numericInput('summary_value_size', 'Value size',
                                                            min = 0, max = 50,
                                                            value = 5, step = 0.25)
                                     ),
                                     column(2, numericInput('summary_text_size', 'Text size',
                                                            min = 0, max = 50,
                                                            value = 15, step = 0.25)
                                     )
                                   )
                                 ),
                                 tags$div(
                                   plotOutput('summary_plot', height = '100%'), #height parameter in all plotOutput() function calls were necessary to make div vertically 'infinite'
                                   class = "plot_container"
                                 )
)


results_venn <- tabPanel("Venn Diagram",
                         actionButton("modify_venn", "Modify plot", class = 'custom_button'),
                         conditionalPanel(
                           condition = "input.modify_venn % 2 == 1",
                           fluidRow(
                             column(2, selectInput('venn_label', 'Label type',
                                                   choices = c(Count = "count",
                                                               Percent = "percent",
                                                               Both = "both",
                                                               None = "none"),
                                                   selectize = FALSE,
                                                   selected = "both" )
                             ),
                             column(2, selectInput('venn_label_color', 'Label color',
                                                   choices = c(Black = "black",
                                                               White = "white"),
                                                   selectize = FALSE,
                                                   selected = "black" )
                             ),
                             column(2, numericInput('venn_label_size', 'Label size',
                                                    min = 1, max = 10,
                                                    value = 4.5, step = 0.5)
                             ),
                             column(2, numericInput('venn_label_alpha', 'Label alpha',
                                                    min = 0, max = 1,
                                                    value = 0.5, step = 0.05)
                             ),
                             column(2, numericInput('venn_set_size', 'Set size',
                                                    min = 1, max = 10,
                                                    value = 4.5, step = 0.5)
                             )
                           )
                         ),
                         tags$div(
                           plotOutput('venn', height = '100%'),
                           class = "plot_container"
                         )
)


#Matybe split the results_upset into a part that contains the modify options and one for the plot itself
results_upset <-  tabPanel("UpSet Plot",
                           #tags$br(),
                           actionButton("modify_upset", "Modify plot", class = 'custom_button'),
                           conditionalPanel(
                             condition = "input.modify_upset % 2 == 1",
                             fluidRow(
                               column(2, numericInput('nintersects', 'Intersects',
                                                      min = 3, max = 150,
                                                      value = 30)
                               ),
                               column(2, selectInput('order.by', 'Order by',
                                                     choices = c(Frequency = "freq",
                                                                 Degree = "degree"
                                                     ),
                                                     multiple = TRUE,
                                                     selected = "freq" )
                               ),
                               column(2, selectInput('scale', 'Scale',
                                                     choices = c(Identity = "identity",
                                                                 log10 = "log10",
                                                                 log2 = "log2"),
                                                     selectize = FALSE,
                                                     selected = "identity" )
                               ),
                               column(2, numericInput('text_size', 'Text size',
                                                      min = 1, max = 3, step = 0.1,
                                                      value = 1.5)
                               ),
                               column(2, numericInput('mb.ratio', 'Barplot size',
                                                      min = 0.1 , max = 0.9, step = 0.05,
                                                      value = 0.7)
                               )
                             ),
                             fluidRow(
                               column(2, selectInput('show.numbers', 'Intersect totals',
                                                     choices = c(Show = "yes",
                                                                 Hide = "no"),
                                                     selectize = FALSE,
                                                     selected = "yes" )
                               ),
                               column(2, selectInput('empty.intersections', 'Empty intersects',
                                                     choices = c(Show = TRUE,
                                                                 Hide = FALSE),
                                                     selectize = FALSE,
                                                     selected = TRUE)
                               )
                             )
                           ),
                           tags$br(),
                           tags$div(
                             plotOutput('upset', height = '100%'),
                             class = "plot_container"
                           )
)

merge_files_panel_title <-
  tagList(
    tags$div("Merging files", class = "custom_title"),
    tags$hr()
  )

merge_files_ui <- sidebarLayout(
  sidebarPanel( width = 3,
                merge_files_panel_title,
                div(class = "justified_text",
                    HTML('Biblioverlap accepts a single csv file for each dataset.
                                  However, there are cases when a query has to be split between multiple files. <br> <br>
                                  In this page, the user can upload multiple csv files (from the same bibliographical database) and merge all records
                                  into a single file. Duplicates are automatically removed. <br> <br>')
                ),
                tabsetPanel(id = 'merging_user_input',
                            tabPanel('Files',
                                     fileInput('unmerged_files',  'Upload files', multiple = TRUE,
                                               accept = c("text/csv",
                                                          "text/comma-separated-values,text/plain",
                                                          ".csv") ) ),
                            tabPanel('Sep',
                                     selectInput('unmerged_sep', 'Separator',
                                                 choices = c(Comma = ",",
                                                             Semicolon = ";",
                                                             Tab = "\t"),
                                                 selectize = FALSE,
                                                 selected = "," ) )
                ),
                downloadButton('download_merged_file', "Download Merged File", width = '100%', class = 'custom_button')
  ),
  mainPanel( width = 9,
             DT::dataTableOutput('merged_files_table') )
)



########################################### DEFINING UI #######################################################

ui <- fluidPage(
  custom_styles,
  favicon,
  title = 'Biblioverlap',
  navbarPage('Biblioverlap',
            id = 'tabs',
    tabPanel('Input Data',
      sidebarLayout(
        sidebarPanel( width = 3,
          input_data_panel_title,
          column_names_ui,
          tags$hr(),
          score_matching_options_ui,
          tags$hr(),
          n_threads_ui,
          tags$hr(),
          n_sets_ui,
          actionButton('submit', "Submit", width = '100%', class = 'custom_button')
        ),
        mainPanel( width = 9,
          conditionalPanel(
            condition = "output.calculation_done",
          tabsetPanel(
            id = "results",
            results_data,
            results_summary_table )
          )
          )
        )
      ),
    tabPanel('Plots',
             sidebarLayout(
               sidebarPanel( width = 3,
                             plot_panel_title,
                             plot_settings
                             ),
               mainPanel( width = 9,
                          conditionalPanel(
                            condition = "output.calculation_done",
                            tabsetPanel(
                              id = 'plots',
                              results_summary_plot,
                              results_venn,
                              results_upset )
                            )
                          )
               )
             ),

    tabPanel('Merge Files',
             merge_files_ui
             )
    )
)