Nothing
################################################################################
# Define UI ####################################################################
shinyUI(pageWithSidebar(
# Application title
headerPanel(windowTitle="Density based peak picking",title="enviPick 1.0"),
sidebarPanel(
fileInput("file1", "Choose centroided .mzXML input file"),
radioButtons("MSlevel", "MS level", c("1"="1","2"="2"), selected = NULL),
actionButton("Calculate","Calculate"),
tags$h6("Progress:"),
verbatimTextOutput("text2"),
verbatimTextOutput("error"),
tags$h6("Job status:"),
verbatimTextOutput("text3"),
verbatimTextOutput("text4"),
verbatimTextOutput("text1"),
verbatimTextOutput("text5")
),
mainPanel(
tags$h4("Parameter settings"),
tabsetPanel(
tabPanel("(1) EIC partitioning & clustering",
sliderInput("drtgap", "Maximum retention time gap in an EIC", min = 20, max = 1500, value = 300, step= 1),
#sliderInput("drtdens1", "Retention time (RT) tolerance for clustering; defined as (+/-) seconds relative to the lowest and highest RT value in each cluster ", min = 10, max = 1500, value = 60, step= 1),
sliderInput("dmzdens", "Maximum deviation (+/-) of m/z of a measurement from its EIC mean [ppm]", min = 1, max = 20, value = 3.5, step= 0.1)
),
tabPanel("(2) Peak definition",
numericInput("minpeak", "Minimum number of measurements per peak ...", 4),
sliderInput("drtsmall2", "... within a given RT window [s]", min = 5, max = 200, value = 20, step= 0.1),
sliderInput("drtfill", "Maximum RT gap length to be interpolated [s]", min = 0, max = 60, value = 10, step= 0.1),
sliderInput("drtdens2", "Peak definition - Maximum RT length of a single peak", min = 10, max = 1500, value = 120, step= 0.1),
sliderInput("minint", "Minimum log10(intensity) threshold", min = 0, max = 10, value = 4, step= .1),
numericInput("SN", "Minimum Signal/Noise", 5),
numericInput("SB", "Minimum Signal/Base", 2),
numericInput("recurs", "Maximum possible number of peaks within a single EIC", 3)
),
tabPanel("(3) Advanced",
numericInput("ended", "How often can a peak detection fail to end the recursion? - peak picking", 1),
numericInput("weight", "Weight for assigning measurements to a peak - peak picking", 1),
sliderInput("maxint", "Upper log10(intensity) safety threshold", min = 0, max = 15, value = 6.7, step= .1),
selectInput("ion_mode", "Polarity (ion mode)", choices=c("FALSE","positive","negative"),selected="FALSE",multiple = FALSE)
)
),
conditionalPanel(
condition = "output.text4 == 'calculation completed'",
tags$h4("Results"),
tabsetPanel(
tabPanel("Summary",
tags$h6("Total number of measurements:"),
verbatimTextOutput("sum_1"),
tags$h6("Number of partitions:"),
verbatimTextOutput("sum_2"),
tags$h6("Number of measurements in partitions:"),
verbatimTextOutput("sum_3"),
tags$h6("Number of EICs:"),
verbatimTextOutput("sum_4"),
tags$h6("Number of measurements in EICs:"),
verbatimTextOutput("sum_5"),
tags$h6("Number of peaks:"),
verbatimTextOutput("sum_6"),
tags$h6("Number of measurements in peaks:"),
verbatimTextOutput("sum_7")
),
tabPanel("Plot",
plotOutput("plotit1"),
plotOutput("plotit2"),
plotOutput("plotit3"),
plotOutput("plotit4"),
actionButton("iRplot","Start interactive R plot")
),
tabPanel("Peak table & download",
downloadButton('downloadData', 'Download'),
tableOutput("peaks")
)
)
)
)
))
################################################################################
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