inst/shiny_app/ui/uiDataInput.R

In svalvaro/MQanalyser: Analyse the proteomics LC-MS/MS data from MaxQuant.

uiDataInput <-  tabPanel(
    h4('Data \nInput'),

    sidebarLayout(
        sidebarPanel(
            id = 'sidebar',
            width = 2,

            shinyjs::useShinyjs(),

            fileInput(
                inputId = 'proteinInput',
                label = h4('Upload the proteinGroups.txt or
                                 proteoQuant.csv'),
                multiple = FALSE,
                accept = 'text'
            ),

            uiOutput('intensity_selector'),

            hr(),

            fileInput(
                inputId = 'optional_exp_design',
                label = h4('Provide the experiment design (Optional)'),
                multiple = FALSE,
                accept = 'text'
            ),
            br(),

            fileInput(
                inputId = 'user_genes',
                label = h4(
                    'Provide a list of desired genes to check
                      in the analysis: (Optional)'
                ),
                multiple = FALSE,
                accept = 'text'
            ),
            hr(),
            br(),

            actionBttn(
                inputId = 'Demo',
                label = 'Start Demo',
                icon = NULL,
                style = "unite",
                color = "default",
                size = "md",
                block = FALSE,
                no_outline = TRUE
            ),

            #Download a file example
            h4('Exapmles of the file(s) to be uploaded:'),


            tags$a(
                href = 'data/proteinGroups_example.txt',
                h5('proteinGroups'),
                download = NA,
                target = '_blank'
            ),

            tags$a(
                href = 'data/user_genes_examples.txt',
                h5('Genes example'),
                download = NA,
                target = '_blank'
            ),
            tags$a(
                href = 'data/experiment_design_example.txt',
                h5('experiment Design'),
                download = NA,
                target = '_blank'
            )

        ),

        mainPanel(
            fluidRow(
                column(
                    width = 4,
                    shinydashboard::infoBoxOutput('softwareUsedBox', width = 12)
                ),

                column(
                    width = 4,
                    shinydashboard::infoBoxOutput('intensityBox',
                                                  width = 12)
                ),
                column(
                    4,
                    shinydashboard::infoBoxOutput('matrixDimensions',
                                                  width = 12),
                )
            ),

            fluidRow(
                column(width = 3),
                column(
                    width = 7,
                    box(
                        title = h3('Experiment Design'),
                        width = 10,
                        h4('Welcome to analysis of the results
                        of LC-MS/MS'),
                        h5('Start by uploading the proteinGroups.txt
                        table provided.'),
                        h5('Please Edit the next table by adding the
                        Condition and Replicate.'),
                        h5(
                            'Alternatively an experiment design can
                        be uploaded. Be sure that the Sample
                        names are correct.'
                        ),
                        hr(),

                        rHandsontableOutput('ed_out'),
                        br(),

                        uiOutput('downloaderExperimentUI')
                    )
                ),
                column(
                    width = 2,
                    br(),
                    br(),
                    br(),
                    br(),
                    br(),
                    br(),

                    uiOutput('start_analysis')
                )
            )
        )
    ),

    # Footer -------------------------------
    br(),
    hr(style = "border-color: #cbcbcb;"),

    fluidRow(column(
        9,

        p(
            "App created by ",
            tags$a(href = "https://www.linkedin.com/in/svalvaro/",
                   'Alvaro Sanchez-Villalba',
                   target = '_blank'),
            HTML("&bull;"),
            style = "font-size: 85%"
        ),

        p(
            "Have a question? Spot an error? Send an email ",
            tags$a(
                href = "mailto:alvaro.sanchez@fgu.cas.cz",
                tags$i(class = 'fa fa-envelope',
                       style = 'color:#990000'),
                target = '_blank'
            ),
            style = "font-size: 85%"
        ),
        p(tags$em("Last updated: March 2022"),
          style = 'font-size:75%')
    ))
)