R/ui.R

In ndmeulem/PeptidoformVisualisation: Visualisation of quantitative peptidoform data

#' Shiny app server object
#' @import shiny shinyhelper shinyWidgets DT plotly shinybusy BiocManager
# create the shiny application user interface

library(shiny)
library(shinyhelper)
library(DT)
library(plotly)
library(shinybusy)
library(shinyWidgets)


ui <- function() {
    shiny::addResourcePath("PeptidoformViz", system.file("helpfiles", package="PeptidoformViz"))
    shinyjs::useShinyjs()

    (navbarPage(

    # Application title
    title = "Visualisation",

    # Add the tabs you want present in the app
    #First tab: upload necessary data files
    tabPanel(title = "Data input",

         add_busy_spinner(spin = "flower",
                          position = "full-page"),

         #Example data button
         fluidRow(
             column(width=4,
                    helper(shinyWidgets::actionBttn(inputId = "example_data",
                                 label = "Read in example data",
                                 color = "royal",
                                 style="bordered",
                                 size = "sm"),
                    type = "markdown", content = "example_data"))
         ),

         #Text output when example data has been read in
         fluidRow(
             column(width=4,
                    textOutput("read_in_example_data"))
         ),

         br(),

         # Show two input data columns

         # Input intensity file
         fluidRow(
             column(width = 6,
                helper(fileInput(inputId = "data", label = "Upload intensity file"),
                    type = "markdown", content = "peptidesfile")),

         # Input metadata file
            column(width = 6,
                helper(fileInput(inputId = "metadata", label = "Upload metadata file"),
                       type = "markdown", content = "metadatafile"))
         ),

        #Now add another row for input reading options
        fluidRow(
            #Options for the peptides intensity file
            column(width = 6,
                   tags$div(tags$h4("Options")),
                   checkboxInput(inputId = "header", label = "header"),
                   numericInput(inputId = "skip", label = "Number of lines to skip", value=0, min=0),
                   radioButtons(inputId = "separator", label = "File separator",
                                choices = c("comma" = ",",
                                            "space" = " ",
                                            "semicolon" = ";",
                                            "tab" = "\t")),
                   textInput(inputId = "intensityIdentifier", label = "Intensity columns identifier"),
                   numericInput(inputId = "proteinColumn", label = "Protein column", value=1, min=1),
                   numericInput(inputId = "sequenceColumn", label = "Sequence column", value=2, min=1),
                   numericInput(inputId = "modificationsColumn", label = "Modifications column", value=3, min=1)
                   ),
            #Option for the metadata file
            column(width = 5,
                   tags$div(tags$h4("Options")),
                   radioButtons(inputId = "separatorMetadata", label = "file separator",
                                choices = c("comma" = ",",
                                            "space" = " ",
                                            "semicolon" = ";",
                                            "tab" = "\t"))
                   )
        ),
        #Add action button for reading in the data
        fluidRow(
            column(width=4,offset=8,
                   shinyWidgets::actionBttn(inputId = "go",
                                label = "Read in your own data",
                                style="bordered",
                                color="royal",
                                size="sm"))
        ),
        #Text output for when data has been read in
        fluidRow(
            column(width=4,offset=8,
                   textOutput("read_in_data"))
        )),

    #Second tab: preprocessing: options + visualisations
    tabPanel(title = "Preprocessing",

         add_busy_spinner(spin = "fading-circle"),
         #Add row for preprocessing options
         fluidRow(
             column(width = 3,
                helper(tags$div(tags$h4("Preprocessing options")),
                       type = "markdown", content = "preprocessingoptions"),

                    radioButtons(inputId = "logTransform",
                      label = "Logarithmic transformation",
                      choiceNames = c("none","log2", "log10", "natural"),
                      choiceValues = c("none", 2, 10, exp(1)))
                ),
             column(width = 3,
                    numericInput(inputId = "nnonzero",
                                 label = "Minimum number of nonzero columns", value=2, min=0),
                    radioButtons(inputId = "normalisationMethodGlobal",
                                 label = "Normalisation",
                                 choices = c("none","center.mean", "center.median")
                                 )
                ),
             column(width = 3,
                    tags$div(tags$h4("Stats before preprocessing")),
                    tableOutput("statstable")),
             column(width = 3,
                    tags$div(tags$h4("Stats after preprocessing")),
                    tableOutput("statstableafter")
                    )
            ),
         #Add row for preprocessing button
         fluidRow(
             column(width=4,offset=4,
                    actionButton(inputId = "preprocess",
                                 label = "Preprocess!",
                                 style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))
         ),
         #Add row for before plots
         fluidRow(
             column(width = 6,
                    tags$div(tags$h4("Density plot before preprocessing")),
                    plotlyOutput("densityBefore")
                    ),
             column(width = 6,
                    tags$div(tags$h4("Density plot after preprocessing")),
                    plotlyOutput("densityAfter")
                    )
            ),
         #Add row for after plots
         fluidRow(
             column(width = 6,
                    tags$div(tags$h4("Boxplot before preprocessing")),
                    plotOutput("boxplotBefore")
             ),
             column(width = 6,
                    tags$div(tags$h4("Boxplot after preprocessing")),
                    plotOutput("boxplotAfter")
             )
         )
         ),

    #Third tab: actual data visualisation
    tabPanel(title = "Data Visualisation",

        add_busy_spinner(spin = "fading-circle"),

        #Add row for protein dropdown menu, normalisation options and data table
        fluidRow(
            #Protein dropdown menu and normalisation options
            column(width = 3,
                tags$div(tags$h4("Protein dropdown menu")),
                selectInput(inputId = "protein", label = "select protein", choices = ""),
                helper(radioButtons(inputId = "normalisationMethod",
                                    label = "Usage options",
                             choiceNames = c("absolute abundance",
                                             "relative abundance (center mean)",
                                             "relative abundance (center median)"),
                             choiceValues = c("none","center.mean", "center.median")),
                       type = "markdown", content = "normalisationfile")
                ),
            #Data table
            column(width = 9,
                   tags$div(tags$h4("Corresponding protein data table")),
                   DTOutput("proteinDataTable"))
            ),
        fluidRow(column(width = 3, offset=2,
                        actionButton(inputId = "deselect",
                                     label = "Deselect all features",
                                     style="color: #fff; background-color: #337ab7; border-color: #2e6da4"))),
        #Add row for the plots themselves
        fluidRow(
            column(width = 6,
                   tags$div(tags$h4("Lineplot of log-normalised features")),
                   plotlyOutput("lineplot")
                   ),
            column(width = 6,
                   tags$div(tags$h4("Boxplot of selected features")),
                   plotlyOutput("boxplot")
                   )
            ),
        #Add row for the arrange x-axis dropdown menu
        fluidRow(
            column(width = 3,
                   tags$div(tags$h4("Arrange x-axis based on")),
                   selectInput(inputId = "x_axis", label = "select variable", choices = ""))
        )
        )
    )
)
}