inst/shiny-app/findMarkersApp/ui.R

In usnistgov/peprDnaStability: For Analysis of NIST Genomic DNA PFGE Gels Images

# This is the user-interface definition of a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com

shinyUI(fluidPage(

    ## Application title
    titlePanel("Stability Gel Processing"),

    ## layout
    fluidRow(
        column(width = 2,
               fileInput('gel_file', 'Choose jpeg File',
                         accept=c('jpg/jpeg','.jpg','.jpeg'))),
        column(width = 2,
               numericInput('lanes','Enter Number of Lanes in the Gel',
                            value = 12, min = 1, max = 14, step = 1)),
        column(width = 4,
               checkboxGroupInput("ladder_lanes", "Select Lanes with Ladders",
                                  choices = list("Lane 1" = 1, "Lane 2" = 2, "Lane 3" = 3,
                                                 "Lane 4" = 4, "Lane 5" = 5, "Lane 6" = 6,
                                                 "Lane 7" = 7, "Lane 8" = 8, "Lane 9" = 9,
                                                 "Lane 10" = 10, "Lane 11" = 11, "Lane 12" = 12),
                                  selected = c(1),
                                  inline = TRUE))
    ),
    fluidRow(
        column(width = 4,
               plotOutput('gel')),
        column(width = 4,
               plotOutput('lanes'))#use offset = X to offset to left
    ),
    fluidRow(
        column(width = 4,
               sliderInput("bw_R1", "Bin Width Region 1",
                           min = 1, max = 100, value = 5),
               sliderInput("bw_R2", "Bin Width Region 2",
                           min = 1, max = 100, value = 5),
               sliderInput("bw_R3", "Bin Width Region 3",
                           min = 1, max = 100, value = 5)),
        column(width = 4,
               sliderInput("npeaks_R1", "Number of Peaks Region 1",
                           min = 1, max = 10, value = 4),
               sliderInput("npeaks_R2", "Number of Peaks Region 2",
                           min = 1, max = 10, value = 3),
               sliderInput("npeaks_R3", "Number of Peaks Region 3",
                           min = 1, max = 10, value = 2)),
        column(width = 4,
               sliderInput("leftset", "Left Offset", min = 0, max = 500, value = 10),
               sliderInput("R1", "Region 1 Right Bound",
                           min = 0, max = 2000, value = 500),
               sliderInput("R2", "Region 2 Right Bound",
                           min = 0, max = 2000, value = 1000),
               sliderInput("R3", "Region 3 Right Bound",
                           min = 0, max = 2000, value = 2000))
    ),
    fluidRow(
        column(width = 8,
               plotOutput('ladder')),
        # image dowloaded from
        # https://www.neb.com/products/n0350-low-range-pfg-marker
        column(2, img(src = "ladder.png")),
        column(width = 2,
               h6("Select same number of markers as number of peaks"),
               checkboxGroupInput('markers', 'Marker Size in kb',
                                  choices = c(194,145.5,97,48.5,23.1,9.42,6.55,4.36,2.32,2.03),
                                  selected = 194),
               downloadButton('downloadData', 'Download Data'),
               downloadButton('downloadParams', 'Download Rdata'))
    ),
    fluidRow(
        column(width = 12,
               dataTableOutput('markerTable')))
    )
)

## Tabbed layout
# shinyUI(navbarPage("Stability Gel Processing",
#                    tabPanel("Gel Lane Edges",
#                             fluidRow(
#                                 column(width = 2,
#                                        fileInput('gel_file',
#                                                  'Choose jpeg File',
#                                                  accept=c('jpg/jpeg','.jpg','.jpeg'))),
#                                 column(width = 2,
#                                        numericInput('lanes',
#                                                     'Enter Number of Lanes in the Gel',
#                                                     value = 12, min = 1, max = 14, step = 1)),
#                                 column(width = 4,
#                                        checkboxGroupInput("ladder_lanes",
#                                                           "Select Lanes with Ladders",
#                                                           choices = list("Lane 1" = 1,
#                                                                          "Lane 2" = 2,
#                                                                          "Lane 3" = 3,
#                                                                          "Lane 4" = 4,
#                                                                          "Lane 5" = 5,
#                                                                          "Lane 6" = 6,
#                                                                          "Lane 7" = 7,
#                                                                          "Lane 8" = 8,
#                                                                          "Lane 9" = 9,
#                                                                          "Lane 10" = 10,
#                                                                          "Lane 11" = 11,
#                                                                          "Lane 12" = 12),
#                                                           selected = c(1,8),
#                                                           inline = TRUE))
#                             ),
#                             fluidRow(
#                                 column(width = 4,
#                                        plotOutput('gel')),
#                                 column(width = 4,
#                                        plotOutput('lanes'))#use offset = X to offset to left
#                             )),
#                    tabPanel("Set Marker ID Parameters",
#                             fluidRow(
#                                 column(width = 4,
#                                        sliderInput("bw_R1", "Bin Width Region 1",
#                                                    min = 1, max = 100, value = 5),
#                                        sliderInput("bw_R2", "Bin Width Region 2",
#                                                    min = 1, max = 100, value = 5),
#                                        sliderInput("bw_R3", "Bin Width Region 3",
#                                                    min = 1, max = 100, value = 5)),
#                                 column(width = 4,
#                                        sliderInput("npeaks_R1", "Number of Peaks Region 1",
#                                                    min = 1, max = 10, value = 4),
#                                        sliderInput("npeaks_R2", "Number of Peaks Region 2",
#                                                    min = 1, max = 10, value = 3),
#                                        sliderInput("npeaks_R3", "Number of Peaks Region 3",
#                                                    min = 1, max = 10, value = 2)),
#                                 column(width = 4,
#                                        sliderInput("leftset", "Left Offset",
#                                                    min = 0, max = 500, value = 10),
#                                        sliderInput("R1", "Region 1 Right Bound",
#                                                    min = 0, max = 2000, value = 500),
#                                        sliderInput("R2", "Region 2 Right Bound",
#                                                    min = 0, max = 2000, value = 1000),
#                                        sliderInput("R3", "Region 3 Right Bound",
#                                                    min = 0, max = 2000, value = 2000))
#
#                             ),
#                             fluidRow(
#                                 column(width = 8,
#                                        plotOutput('ladder')),
#                                 # image dowloaded from
#                                 # https://www.neb.com/products/n0350-low-range-pfg-marker
#                                 column(2, img(src = "ladder.png")),
#                                 column(width = 2,
#                                        h6("Select same number of markers as number of peaks"),
#                                        checkboxGroupInput('markers', 'Marker Size in kb',
#                                                           choices = c(194,145.5,97,48.5,23.1,
#                                                                       9.42,6.55,4.36,2.32,2.03),
#                                                           selected = 194)))),
#                    tabPanel("Download Data",
#                             fluidRow(
#                                 column(width = 4,
#                                        downloadButton('downloadData', 'Download Data')),
#                                 column(width = 4,
#                                        downloadButton('downloadParams', 'Download Rdata'))
#                             ),
#                             fluidRow(
#                                 column(width = 12,
#                                        dataTableOutput('markerTable')))
#                    )
# ))