give shiny a try; to run this example: `install.packages("shiny"); library("shiny"); runGist("5725234")`

server.R

library("shiny")

library("MALDIquant")

data("fiedler2009subset")

shinyServer(function(input, output) {

  output$plotBaseline <- renderPlot({
    plot(fiedler2009subset[[1]])
    lines(estimateBaseline(fiedler2009subset[[1]],
                           method=input$bem, input$hws), col=2, lwd=2)
  })
})

ui.R

library("shiny")

shinyUI(pageWithSidebar(

  headerPanel("MALDIquant - Baseline Estimation"),

  sidebarPanel(
    radioButtons("bem", 'Baseline Estimation Method:',
                 c(SNIP="SNIP",
                   TopHat="TopHat",
                   ConvexHull="ConvexHull",
                   Median="median"),
                 "SNIP"),
    sliderInput("hws",
                "halfWindowSize:",
                min = 1,
                max = 1000,
                value = 100)
  ),

  mainPanel(
    plotOutput("plotBaseline")
  )
))