inst/shiny/Imetagene/ui.R

In andronekomimi/Imetagene: A graphical interface for the metagene package

# IMETAGENE UI.R
library(shiny)
library(shinyBS)
library(shinythemes)
library(plotly)

footer<-function(){
  tags$div(
    class = "footer",
    style = "text-align:center",
    tags$div(class = "foot-inner",
             list(
               hr(),
               "Imetagene is an ", 
               tags$a(href="http://bioinformatique.genome.ulaval.ca/recherche/","Arnaud Droit Lab"),
               " project (2015).",
               br(),
               "Development of Imetagene web interface ",
               tags$a(href="https://ca.linkedin.com/in/audreylemacon", "Audrey Lemacon "),
               br(),
               "Development of metagene library : ",
               tags$a(href="https://ca.linkedin.com/pub/charles-joly-beauparlant/89/491/3b3", "Charles Joly-Beauparlant ")
             )
             
    )
  )
}

app_name = "Imetagene"

shinyUI(fluidPage(theme = shinythemes::shinytheme("flatly"),
  tags$head(
    tags$style(
      HTML("     
      h1 {
          font-family: 'Courier New', Courier, monospace;
      }
      .navbar-brand {
          font-family: 'Courier New', Courier, monospace;
          float:left;
      }
    ")
    ),
    tags$script('Shiny.addCustomMessageHandler("myCallbackHandler",
       function(typeMessage) {console.log(typeMessage)
           if(typeMessage == 1){
              $("a:contains(DESIGN)").click();
           } else {
              if(typeMessage == 2) {
                  $("a:contains(MATRIX)").click();
              } else {
                if(typeMessage == 3) {
    $("a:contains(PLOT)").click();
                }
              }
           }
        });')  
    
  ),
  
  headerPanel(app_name),
  sidebarLayout(
    NULL,
    mainPanel(
      p("This application enables to use interactively the metagene package.
        This R package produces Metagene-like plots to compare the behavior of 
        DNA-interacting proteins at selected groups of features."),
      fluidRow(
        column(width = 12,
               navbarPage("Imetagene",
          tabPanel("INPUTS",
                   shinyBS::bsCollapse(id = "inputs", 
                       open = c("Load existing metagene object"), 
                       multiple = FALSE,
                       shinyBS::bsCollapsePanel("Load existing metagene object", 
                list(
                  helpText("Load a metagene object produced during a previous session."),
                  shiny::actionLink(inputId = "hloadMetagene", label = "", icon = icon("question-circle")),
                  fileInput('path_load_metagene', 'Choose file to upload',
            width = '60%',
            accept = c(
              '.Rda', 
              '.RData', 
              '.RDA', 
              '.RDATA'
            )
                  ),
                  # shinyFiles::shinyFilesButton('loadMetagene', 'Choose file',
                  #              'Please select a file', FALSE),
                  # textInput(inputId = "path_load_metagene", label = "", width = "100%"),
                  shinyBS::bsAlert("load_alert")
                ), 
                style = "primary"),
                       shinyBS::bsCollapsePanel("Create a new metagene object", 
                list(
                  helpText("Create a metagene object from scratch with indexed BAM and BED files."),
                  fluidRow(
                    column(width = 4,
                           list(
             shiny::actionLink(inputId = "hbams", label = "", icon = icon("question-circle")),
             br(),
             br(),
             fileInput('file1', 'Select BAM files',
                       width = '100%',
                       multiple = TRUE,
                       accept = c('.bam')
             ),
             uiOutput("bam_list")
                           )
                    ),
                    column(width = 4,
                           list(
             shiny::actionLink(inputId = "hbais", label = "", icon = icon("question-circle")),
             br(),
             br(),
             fileInput('file2', 'Select corresponding BAI files',
                       width = '100%',
                       multiple = TRUE,
                       accept = c('.bai')
             ),
             uiOutput("bai_list")
                           )
                    ),
                    column(width = 4,
                           list(
             shiny::actionLink(inputId = "hbeds", label = "", icon = icon("question-circle")),
             br(),
             br(),
             fileInput('file3', 'Select BED files',
                       width = '100%',
                       multiple = TRUE,
                       accept = c('.bed', 
                  '.BED', 
                  '.narrowPeak', 
                  '.broadPeak')
             ),
             uiOutput("bed_list")
                           )
                    )
                  ),
                  br(),hr(),br(),
                  fluidRow(
                    column(width = 6,
                           shinyBS::bsButton(inputId = "runMetagene", label = "Run metagene", style = "btn btn-primary", disabled = FALSE)),
                    column(width = 6,
                           downloadButton(outputId = "saveMetagene", label = "Save metagene", class = "btn btn-primary"))
                  ),
                  br(),
                  shinyBS::bsAlert("run_alert"),
                  uiOutput(outputId = "resizingUI")
                ), 
                style = "primary")
                   ),
                   shinyBS::bsButton(inputId = "go2design", label = "Next step", style = "btn btn-primary", disabled = TRUE, icon = icon("arrow-right"))
          ),
          tabPanel("DESIGN",
                   shinyBS::bsCollapse(id = "design", 
                       open = c("Current design"), 
                       multiple = TRUE,
                       shinyBS::bsCollapsePanel("Current design", 
                list(
                  fluidRow(
                    column(width = 12,
                           list(
             helpText("Here is the design contained in the current metagene if any."),
             dataTableOutput('current_mg_design')
                           )
                    )
                  )
                ), 
                style = "primary"),
                       shinyBS::bsCollapsePanel("Load existing design file", 
                list(
                  fluidRow(
                    column(width = 8,
                           list(
             shiny::actionLink(inputId = "hloadDesign", label = "", icon = icon("question-circle")),
             br(),
             br(),
             fileInput('file4', 'Select design file',
                       width = '100%',
                       multiple = TRUE,
                       accept = c('',
                  '.txt',
                  '.tsv')
             )
                           )
                    ),
                    column(width = 3,
                           list(
             checkboxInput(inputId = "header", label = "File with header", value = TRUE)
                           )
                    )
                  ),
                  shinyBS::bsAlert("load_alert_d")
                ), 
                style = "primary"),
                       shinyBS::bsCollapsePanel("Create a new design", 
                list(
                  textInput(inputId = "exp_name", label = "Experience name", value = "Exp1"),
                  fluidRow(
                    column(width = 6,
                           list(
             selectInput(inputId = "chips", 
                         label = "Select the ChIP for your experiment",
                         selected = NULL,
                         multiple = TRUE,
                         width = '100%',
                         selectize = TRUE,
                         choices = c(''))
                           )
                    ),
                    column(width = 6,
                           list(
             selectInput(inputId = "ctrls", 
                         label = "Select the associated controls for your experiment",
                         selected = NULL,
                         multiple = TRUE,
                         width = '100%',
                         selectize = TRUE,
                         choices = c(''))
                           )
                    )
                  ),
                  br(),br(),
                  shinyBS::bsAlert("save_exp_alert"),
                  shinyBS::bsButton(inputId = "saveExp", label = "Save Experiment", style = "btn btn-primary", disabled = FALSE),
                  br(),br(),
                  downloadButton(outputId = "saveDesign", label = "Save Current Design")
                ), 
                style = "primary")
                   ),
                   shinyBS::bsButton(inputId = "go2matrix", label = "Next step", style = "btn btn-primary", disabled = FALSE, icon = icon("arrow-right"))
          ),
          tabPanel("MATRIX",
                   helpText("In order to represent the genomic coverages in a metagene plot, the coverages must be converted in matrix format. Regions are binned to reduce computation time for the following steps. During this step, the noise can be removed using one or more controls and the coverages can be normalized to allow comparison of multiple experiments."),
                   shinyBS::bsCollapse(id = "matrix", 
                       open = c("Current matrix subset"), 
                       multiple = TRUE,
                       shinyBS::bsCollapsePanel("Current matrix subset",
                list(
                  fluidRow(
                    column(width = 12,
                           list(
             helpText("Here is a subset of the matrix contained in the current metagene if any."),
             verbatimTextOutput('current_mg_matrix_content'),
             uiOutput('current_mg_matrix_heatmap')
                           )
                    )
                  )
                ), 
                style = "primary"),
                       shinyBS::bsCollapsePanel("Matrix parameters", 
                list(
                  fluidRow(
                    column(width = 3,
                           numericInput(inputId = "bin_count", value = 1, label = "bin count")),
                    column(width = 8,
                           shiny::actionLink(inputId = "hbin_count", label = "", icon = icon("question-circle")))
                  ),
                  fluidRow(
                    column(width = 3,
                           selectInput(inputId = "noise", choices = c("NONE","NCIS"), label = "noise removal")),
                    column(width = 8,
                           shiny::actionLink(inputId = "hnoise", label = "", icon = icon("question-circle")))
                  ),
                  fluidRow(
                    column(width = 3,
                           selectInput(inputId = "norm", choices = c("NONE","RPM"), label = "normalization")),
                    column(width = 8,
                           shiny::actionLink(inputId = "hnorm", label = "", icon = icon("question-circle")))
                  ),
                  fluidRow(
                    column(width = 3,
                           checkboxInput(inputId = "flip", value = FALSE, label = "flip regions")),
                    column(width = 8,
                           shiny::actionLink(inputId = "hflip", label = "", icon = icon("question-circle")))
                  ),
                  fluidRow(
                    column(width = 3,
                           checkboxInput(inputId = "use_design", value = TRUE, label = "use design")),
                    column(width = 8,
                           shiny::actionLink(inputId = "huse_design", label = "", icon = icon("question-circle")))
                  ),
                  br(),
                  fluidRow(
                    column(width = 3,
                           shinyBS::bsButton(inputId = "runMatrix", label = "Produce matrix", style = "btn btn-primary", disabled = FALSE)),
                    column(width = 8,
                           downloadButton(outputId = "updateMetagene", label = "Save metagene", class = "btn btn-primary"))
                  ),
                  br(),
                  shinyBS::bsAlert("run_matrix_alert")
                )
                ,style = "primary"
                       )
                   ),
                   shinyBS::bsButton(inputId = "go2plot", label = "Next step", style = "btn btn-primary", disabled = FALSE, icon = icon("arrow-right"))
          ),tabPanel("PLOT",
                     helpText("Produce a metagene plot."),
                     shinyBS::bsCollapse(id = "plot", 
         open = c("Plot parameters"), 
         multiple = FALSE,
         shinyBS::bsCollapsePanel("Plot parameters", 
                  list(
                    fluidRow(
                      column(width = 4,
             list(
               selectInput(inputId = "plot_regions", 
                           label = "Regions to display",
                           selected = NULL,
                           multiple = TRUE,
                           width = '75%',
                           selectize = TRUE,
                           choices = c("")),
               selectInput(inputId = "plot_exps", 
                           label = "Experiments to display",
                           selected = NULL,
                           multiple = TRUE,
                           width = '75%',
                           selectize = TRUE,
                           choices = c("")),
               textInput(inputId = "plot_title", label = "plot title", value = "Enter text..."),
               fluidRow(
                 column(width = 9,
                        sliderInput(inputId = "alpha", label = "alpha", min = 0, max = 1, value = 0.05)),
                 column(width = 3,
                        shiny::actionLink(inputId = "halpha", label = "", icon = icon("question-circle")))
               ),
               fluidRow(
                 column(width = 9,
                        numericInput(inputId = "sample_count", label = "sample count",value = 1000)),
                 column(width = 3,
                        shiny::actionLink(inputId = "hsample_count", label = "", icon = icon("question-circle")))
               )
             )
                      ),
                      column(width = 8,
             list(
               plotlyOutput(outputId = "mg_plot")
             )
                      )
                    ),
                    br(),
                    shinyBS::bsButton(inputId = "runPlot", label = "Plot", style = "btn btn-primary", disabled = FALSE),
                    br()
                  )
                  ,style = "primary"
         )
                     )
          )
               )
        )
      ), width="100%",footer()
    )
  )
))