Upgrade to new Gitlab Version 13.9 on Saturday 19th April 20:00. Expect an interruption of about 30 to 60 minutes

tabAUC.R 2.29 KB
Newer Older
dmattek's avatar
dmattek committed
1 2 3 4 5 6
#
# Time Course Inspector: Shiny app for plotting time series data
# Author: Maciej Dobrzynski
#
# This module is a tab for plotting Area Under Curve
#
dmattek's avatar
Added:  
dmattek committed
7 8 9 10
# Calculates area under curve (AUC) for every single time course provided in the input

require(pracma) # for trapz

dmattek's avatar
dmattek committed
11
# UI ----
dmattek's avatar
Added:  
dmattek committed
12 13 14 15
modAUCplotUI =  function(id, label = "Plot Area Under Curves") {
  ns <- NS(id)
  
  tagList(
16 17 18 19 20 21 22 23 24
    h4(
      "Calculate area under curve and plot per group"
    ),
    br(),
    
    uiOutput(ns('uiSlTimeTrim')),
    modStatsUI(ns('dispStats')),
    br(),
    modBoxPlotUI(ns('boxPlot')
dmattek's avatar
Added:  
dmattek committed
25 26 27 28
    )
  )
}

dmattek's avatar
dmattek committed
29
# SERVER ----
30
modAUCplot = function(input, output, session, in.data, in.fname) {
dmattek's avatar
Added:  
dmattek committed
31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50
  
  ns <- session$ns
  
  # return all unique time points (real time)
  # This will be used to display in UI for box-plot
  # These timepoints are from the original dt and aren't affected by trimming of x-axis
  getDataTpts <- reactive({
    cat(file = stderr(), 'getDataTpts\n')
    loc.dt = in.data()
    
    if (is.null(loc.dt))
      return(NULL)
    else
      return(unique(loc.dt[['realtime']]))
  })
  
  # UI for trimming x-axis (time)
  output$uiSlTimeTrim = renderUI({
    cat(file = stderr(), 'UI uiSlTimeTrim\n')
    
51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67
    locTpts  = getDataTpts()
    
    if(is.null(locTpts))
      return(NULL)
    
    locRTmin = min(locTpts)
    locRTmax = max(locTpts)
    
    sliderInput(
      ns('slTimeTrim'),
      label = 'Select time range for AUC calculation',
      min = locRTmin,
      max = locRTmax,
      value = c(locRTmin, locRTmax),
      step = 1
    )
    
dmattek's avatar
Added:  
dmattek committed
68 69 70 71 72 73 74 75 76 77 78 79 80
  })
  
  AUCcells = reactive({
    cat(file = stderr(), 'AUCcells\n')
    loc.dt = in.data()
    
    if (is.null(loc.dt))
      return(NULL)
    else {
      loc.res = loc.dt[realtime >= input$slTimeTrim[1] & realtime <= input$slTimeTrim[2], .(AUC = trapz(realtime, y)), by = .(group, id)]
      return(loc.res)
    }
  })
81
  
dmattek's avatar
Added:  
dmattek committed
82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103
  callModule(modStats, 'dispStats',
             in.data = AUCcells,
             in.meascol = 'AUC',
             in.bycols = c('group'),
             in.fname = 'data4boxplotAUC.csv')
  
  callModule(modBoxPlot, 'boxPlot', 
             in.data = AUCcells, 
             in.cols = list(meas.x = 'group',
                            meas.y = 'AUC',
                            group = 'group',
                            id = 'id'),
             in.fname = in.fname)
  
  
}