Due to a scheduled upgrade to version 14.10, GitLab will be unavailabe on Monday 30.05., from 19:00 until 20:00.

server.R 15.1 KB
Newer Older
dmattek's avatar
dmattek committed
1

2

dmattek's avatar
dmattek committed
3
4
5
6
7
8
9
10
11
12
13
14
# This is the server logic for a Shiny web application.
# You can find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com
#

library(shiny)
library(shinyjs) #http://deanattali.com/shinyjs/
library(data.table)
library(ggplot2)
library(plotly)

15
16
# increase file upload limit
options(shiny.maxRequestSize = 30 * 1024 ^ 2)
dmattek's avatar
dmattek committed
17
18
source('auxfunc.R')

dmattek's avatar
dmattek committed
19
shinyServer(function(input, output, session) {
20
  useShinyjs()
dmattek's avatar
dmattek committed
21
  
22
23
24
25
26
27
28
29
  # This is only set at session start
  # we use this as a way to determine which input was
  # clicked in the dataInBoth reactive
  counter <- reactiveValues(
    # The value of inDataGen1,2 actionButton is the number of times they were pressed
    dataGen1     = isolate(input$inDataGen1),
    dataLoadNuc  = isolate(input$inButLoadNuc)
    #dataLoadStim = isolate(input$inButLoadStim)
dmattek's avatar
dmattek committed
30
31
  )
  
dmattek's avatar
dmattek committed
32
33
34
  ####
  ## UI for side panel
  
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
  # This button will reset the inFileLoad
  observeEvent(input$inButReset, {
    reset("inFileLoadNuc")  # reset is a shinyjs function
    #reset("inButLoadStim")  # reset is a shinyjs function
  })
  
  # generate random dataset 1
  dataGen1 <- eventReactive(input$inDataGen1, {
    cat("dataGen1\n")
    
    return(userDataGen())
  })
  
  # load main data file
  dataLoadNuc <- eventReactive(input$inButLoadNuc, {
    cat("dataLoadNuc\n")
    locFilePath = input$inFileLoadNuc$datapath
    
    counter$dataLoadNuc <- input$inButLoadNuc - 1
    
    if (is.null(locFilePath) || locFilePath == '')
      return(NULL)
    else {
      return(fread(locFilePath))
    }
  })
  
dmattek's avatar
dmattek committed
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
  # This button will reset the inFileLoad
  observeEvent(input$butReset, {
    reset("inFileLoadNuc")  # reset is a shinyjs function
    #    reset("inFileStimLoad")  # reset is a shinyjs function
    
  })
  

  output$varSelTrackLabel = renderUI({
    cat(file = stderr(), 'UI varSelTrackLabel\n')
    locCols = getDataNucCols()
    locColSel = locCols[locCols %like% 'rack'][1] # index 1 at the end in case more matches; select 1st
    
    cat(locColSel, '\n')
    selectInput(
      'inSelTrackLabel',
      'Select Track Label (e.g. objNuc_Track_ObjectsLabel):',
      locCols,
      width = '100%',
      selected = locColSel
    )
  })
  
  output$varSelTime = renderUI({
    cat(file = stderr(), 'UI varSelTime\n')
    locCols = getDataNucCols()
    locColSel = locCols[locCols %like% 'RealTime'][1] # index 1 at the end in case more matches; select 1st
    
    cat(locColSel, '\n')
    selectInput(
      'inSelTime',
      'Select time column (e.g. RealTime):',
      locCols,
      width = '100%',
      selected = locColSel
    )
  })
  
  # This is main field to select plot facet grouping
  # It's typically a column with the entire experimental description,
  # e.g. in Yannick's case it's Stim_All_Ch or Stim_All_S.
  # In Coralie's case it's a combination of 3 columns called Stimulation_...
  output$varSelGroup = renderUI({
    cat(file = stderr(), 'UI varSelGroup\n')
    locCols = getDataNucCols()
    
    if (!is.null(locCols)) {
      locColSel = locCols[locCols %like% 'ite']
      if (length(locColSel) == 0)
        locColSel = locCols[locCols %like% 'eries'][1] # index 1 at the end in case more matches; select 1st
      else if (length(locColSel) > 1) {
        locColSel = locColSel[1]
      }
      #    cat('UI varSelGroup::locColSel ', locColSel, '\n')
      selectInput(
        'inSelGroup',
        'Select one or more facet groupings (e.g. Site, Well, Channel):',
        locCols,
        width = '100%',
        selected = locColSel,
        multiple = TRUE
      )
    }
    
  })
  
  output$varSelSite = renderUI({
    cat(file = stderr(), 'UI varSelSite\n')
    locCols = getDataNucCols()
    locColSel = locCols[locCols %like% 'ite'][1] # index 1 at the end in case more matches; select 1st
    
    cat(locColSel, '\n')
    selectInput(
      'inSelSite',
      'Select FOV (e.g. Metadata_Site or Metadata_Series):',
      locCols,
      width = '100%',
      selected = locColSel
    )
  })
  
  
  
  
  output$varSelMeas1 = renderUI({
    cat(file = stderr(), 'UI varSelMeas1\n')
    locCols = getDataNucCols()
    
    if (!is.null(locCols)) {
      locColSel = locCols[locCols %like% 'objCyto_Intensity_MeanIntensity_imErkCor.*' | locCols %like% 'Ratio'][1] # index 1 at the end in case more matches; select 1st
      #    cat(locColSel, '\n')
      selectInput(
        'inSelMeas1',
        'Select 1st measurement:',
        locCols,
        width = '100%',
        selected = locColSel
      )
    }
  })
  
  
  output$varSelMeas2 = renderUI({
    cat(file = stderr(), 'UI varSelMeas2\n')
    locCols = getDataNucCols()
    
    if (!is.null(locCols) &&
        !(input$inSelMath %in% c('', '1 / '))) {
      locColSel = locCols[locCols %like% 'objNuc_Intensity_MeanIntensity_imErkCor.*'][1] # index 1 at the end in case more matches; select 1st
      #    cat(locColSel, '\n')
      selectInput(
        'inSelMeas2',
        'Select 2nd measurement',
        locCols,
        width = '100%',
        selected = locColSel
      )
    }
  })
  
  
  ####
  ## data processing
  
  # generate random dataset 1
  dataGen1 <- eventReactive(input$inDataGen1, {
    cat("dataGen1\n")
    
    return(userDataGen())
  })
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
  
  dataInBoth <- reactive({
    # Without direct references to inDataGen1,2 and inFileLoad, inDataGen2
    #    does not trigger running this reactive once inDataGen1 is used.
    # This is one of the more nuanced areas of reactive programming in shiny
    #    due to the if else logic, it isn't fetched once inDataGen1 is available
    # The morale is use direct retrieval of inputs to guarantee they are available
    #    for if else logic checks!
    
    locInGen1 = input$inDataGen1
    locInLoadNuc = input$inButLoadNuc
    #locInLoadStim = input$inButLoadStim
    
    cat(
      "dataInBoth\ninGen1: ",
      locInGen1,
      "   prev=",
      isolate(counter$dataGen1),
      "\ninDataNuc: ",
      locInLoadNuc,
      "   prev=",
      isolate(counter$dataLoadNuc),
      # "\ninDataStim: ",
      # locInLoadStim,
      # "   prev=",
      # isolate(counter$dataLoadStim),
      "\n"
    )
    
    # isolate the checks of counter reactiveValues
    # as we set the values in this same reactive
    if (locInGen1 != isolate(counter$dataGen1)) {
      cat("dataInBoth if inDataGen1\n")
      dm = dataGen1()
      # no need to isolate updating the counter reactive values!
      counter$dataGen1 <- locInGen1
    } else if (locInLoadNuc != isolate(counter$dataLoadNuc)) {
      cat("dataInBoth if inDataLoadNuc\n")
      dm = dataLoadNuc()
      # no need to isolate updating the counter reactive values!
      counter$dataLoadNuc <- locInLoadNuc
    } else {
      cat("dataInBoth else\n")
      dm = NULL
    }
    return(dm)
  })
  
  # return column names of the main dt
dmattek's avatar
dmattek committed
241
  getDataNucCols <- reactive({
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
    cat(file = stderr(), 'getDataNucCols: in\n')
    loc.dt = dataInBoth()
    
    if (is.null(loc.dt))
      return(NULL)
    else
      return(colnames(loc.dt))
  })
  
  # return dt with an added column with unique track object label
  dataMod <- reactive({
    cat(file=stderr(), 'dataMod\n')
    loc.dt = dataInBoth()
    
    if(is.null(loc.dt))
      return(NULL)
    
    loc.dt[, trackObjectsLabelUni := paste(sprintf("%03d", get(input$inSelSite)),
                                           sprintf("%04d", get(input$inSelTrackLabel)),
                                           sep = "_")]
dmattek's avatar
dmattek committed
262
    
263
264
265
    return(loc.dt)
  })
  
dmattek's avatar
dmattek committed
266
267
268
269
270
  # return all unique track object labels (created in dataMod)
  # This will be used to display in UI for trajectory highlighting
  getDataTrackObjLabUni <- reactive({
    cat(file = stderr(), 'getDataTrackObjLabUni\n')
    loc.dt = dataMod()
271
    
dmattek's avatar
dmattek committed
272
273
274
275
    if (is.null(loc.dt))
      return(NULL)
    else
      return(unique(loc.dt$trackObjectsLabelUni))
276
277
  })
  
dmattek's avatar
dmattek committed
278
279
280
281
282
  # return all unique time points (real time)
  # This will be used to display in UI for trajectory highlighting
  getDataTpts <- reactive({
    cat(file = stderr(), 'getDataTpts\n')
    loc.dt = dataMod()
283
    
dmattek's avatar
dmattek committed
284
285
286
287
    if (is.null(loc.dt))
      return(NULL)
    else
      return(unique(loc.dt[[input$inSelTime]]))
288
289
290
291
292
  })
  
  
  # prepare data for plotting time courses
  # returns dt with these columns:
dmattek's avatar
dmattek committed
293
294
295
296
297
298
299
  #    realtime - selected from input
  #    y        - measurement selected from input 
  #               (can be a single column or result of an operation on two cols)
  #    id       - trackObjectsLabelUni (created in dataMod)
  #    group    - grouping variable for facetting from input
  #    mid.in   - column with trajectory selection status from the input file or
  #               highlight status from UI
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
  data4trajPlot <- reactive({
    cat(file=stderr(), 'data4trajPlot\n')
    
    loc.dt = dataMod()
    if(is.null(loc.dt))
      return(NULL)
    
    
    if(input$inSelMath == '')
      loc.s.y = input$inSelMeas1
    else if (input$inSelMath == '1 / ')
      loc.s.y = paste0(input$inSelMath, input$inSelMeas1)
    else
      loc.s.y = paste0(input$inSelMeas1, input$inSelMath, input$inSelMeas2)
    
    # create expression for parsing
    # creates a merged column based on other columns from input
    # used for grouping of plot facets
    loc.s.gr = sprintf("paste(%s, sep=';')", paste(input$inSelGroup, sep = '', collapse = ','))
    
    loc.s.rt = input$inSelTime
    
dmattek's avatar
dmattek committed
322
323
324
325
    # Assign tracks selected for highlighting in UI
    loc.tracks.highlight = input$inSelHighlight
    locBut = input$chBhighlightTraj
    
326
327
328
329
330
331
332
333
334
335
    # if dataset contains column mid.in with trajectory filtering status,
    # then, include it in plotting
    if (sum(names(loc.dt) %in% 'mid.in') > 0) {
      loc.out = loc.dt[, .(
        y = eval(parse(text = loc.s.y)),
        id = trackObjectsLabelUni,
        group = eval(parse(text = loc.s.gr)),
        realtime = eval(parse(text = loc.s.rt)),
        mid.in = mid.in
      )]
dmattek's avatar
dmattek committed
336
337
338
339
340
341
342
      
      # add 3rd level with status of track selection
      # to a column with trajectory filtering status
      if (locBut) {
        loc.out[, mid.in := ifelse(id %in% loc.tracks.highlight, 'SELECTED', mid.in)]
      }
      
343
344
345
346
347
348
349
    } else {
      loc.out = loc.dt[, .(
        y = eval(parse(text = loc.s.y)),
        id = trackObjectsLabelUni,
        group = eval(parse(text = loc.s.gr)),
        realtime = eval(parse(text = loc.s.rt))
      )]
dmattek's avatar
dmattek committed
350
351
352
353
354
      
      # add a column with status of track selection
      if (locBut) {
        loc.out[, mid.in := ifelse(id %in% loc.tracks.highlight, 'SELECTED', 'NOT SEL')]
      }
355
    }
356
357
358
    
    # remove rows with NA
    return(loc.out[complete.cases(loc.out)])
dmattek's avatar
dmattek committed
359
360
  })
  
dmattek's avatar
dmattek committed
361
362
363
364
365
  # prepare data for plotting boxplots
  # uses the same dt as for trajectory plotting
  # returns dt with these columns:
  data4boxPlot <- reactive({
    cat(file=stderr(), 'data4trajPlot\n')
dmattek's avatar
dmattek committed
366
    
dmattek's avatar
dmattek committed
367
368
369
    loc.dt = data4trajPlot()
    if(is.null(loc.dt))
      return(NULL)
dmattek's avatar
dmattek committed
370
    
dmattek's avatar
dmattek committed
371
    loc.out = loc.dt[realtime %in% input$inSelTpts]
dmattek's avatar
dmattek committed
372
373
  })
  
dmattek's avatar
dmattek committed
374
375
  ####
  ## UI for trajectory plot
dmattek's avatar
dmattek committed
376
  
dmattek's avatar
dmattek committed
377
378
  output$varSelHighlight = renderUI({
    cat(file = stderr(), 'UI varSelHighlight\n')
dmattek's avatar
dmattek committed
379
    
dmattek's avatar
dmattek committed
380
381
382
    locBut = input$chBhighlightTraj
    if (!locBut)
      return(NULL)
dmattek's avatar
dmattek committed
383
    
dmattek's avatar
dmattek committed
384
385
    loc.v = getDataTrackObjLabUni()
    if(!is.null(loc.v)) {
386
      selectInput(
dmattek's avatar
dmattek committed
387
388
389
        'inSelHighlight',
        'Select one or more rajectories:',
        loc.v,
390
        width = '100%',
dmattek's avatar
dmattek committed
391
        multiple = TRUE
392
      )
dmattek's avatar
dmattek committed
393
394
395
396
    }
  })
  
  
dmattek's avatar
dmattek committed
397
  output$uiPlotTraj = renderUI({
dmattek's avatar
dmattek committed
398
    
dmattek's avatar
dmattek committed
399
    plotlyOutput("plotTraj", width = paste0(input$inPlotTrajWidth, '%'), height = paste0(input$inPlotTrajHeight, 'px'))
dmattek's avatar
dmattek committed
400
401
  })
  
402
403
  output$plotTraj <- renderPlotly({
    cat(file=stderr(), 'plotTraj: in\n')
dmattek's avatar
dmattek committed
404
    locBut = input$butPlotTraj
dmattek's avatar
dmattek committed
405
406
    
    if (locBut == 0) {
407
      cat(file=stderr(), 'plotTraj: Go button not pressed\n')
dmattek's avatar
dmattek committed
408
409
410
411
      
      return(NULL)
    }
    
412
    loc.dt = isolate(data4trajPlot())
dmattek's avatar
dmattek committed
413
    
414
415
416
    cat("plotScatter on to plot\n\n")
    if (is.null(loc.dt)) {
      cat(file=stderr(), 'plotTraj: dt is NULL\n')
dmattek's avatar
dmattek committed
417
      return(NULL)
dmattek's avatar
dmattek committed
418
419
    }
    
420
    cat(file=stderr(), 'plotTraj:dt not NULL\n')
dmattek's avatar
dmattek committed
421
    
422
423
424
425
426
427
    # colour trajectories, if dataset contains mi.din column
    # with filtering status of trajectory
    if(sum(names(loc.dt) %in% 'mid.in') > 0)
      loc.line.col.arg = 'mid.in'
    else
      loc.line.col.arg = NULL
dmattek's avatar
dmattek committed
428
429
    
    p.out = myGgplotTraj(
430
431
432
433
434
435
      dt.arg = loc.dt,
      x.arg = 'realtime',
      y.arg = 'y',
      group.arg = "id",
      facet.arg = 'group',
      facet.ncol.arg = input$inPlotTrajFacetNcol,
436
437
      xlab.arg = 'Time (min)',
      line.col.arg = loc.line.col.arg
dmattek's avatar
dmattek committed
438
    )
dmattek's avatar
dmattek committed
439
    
dmattek's avatar
dmattek committed
440
    
dmattek's avatar
dmattek committed
441
442
443
444
    # This is required to avoid 
    # "Warning: Error in <Anonymous>: cannot open file 'Rplots.pdf'"
    # When running on a server. Based on:
    # https://github.com/ropensci/plotly/issues/494
dmattek's avatar
dmattek committed
445
446
447
    if (names(dev.cur()) != "null device") dev.off()
    pdf(NULL)
    
dmattek's avatar
dmattek committed
448
449
    p.out.ly = plotly_build(p.out)
    return(p.out.ly)
dmattek's avatar
dmattek committed
450
451
  })
  
dmattek's avatar
dmattek committed
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542

  ####
  ## UI for box-plot
  
  output$varSelTpts = renderUI({
    cat(file = stderr(), 'UI varSelTpts\n')
    
    loc.v = getDataTpts()
    if(!is.null(loc.v)) {
      selectInput(
        'inSelTpts',
        'Select one or more timepoints:',
        loc.v,
        width = '100%', 
        selected = 0,
        multiple = TRUE
      )
    }
  })
  
  # Boxplot - display
  output$outPlotBox = renderPlot({
    
    locBut = input$butPlotBox
    
    if (locBut == 0) {
      cat(file=stderr(), 'plotBox: Go button not pressed\n')
      return(NULL)
    }
    
    plotBox()

  }, height = 800)
  
  # Boxplot - download pdf
  output$downPlotBox <- downloadHandler(
    filename = 'boxplot.pdf',
    
    content = function(file) {
      cat(file = stderr(), input$inPlotBoxWidth, input$inPlotBoxHeight, "\n")
      ggsave(file, limitsize = FALSE,
             plotBox(), 
             width  = input$inPlotBoxWidth,
             height = input$inPlotBoxHeight)
    }
  )
  
  
  # Function instead of reactive as per:
  # http://stackoverflow.com/questions/26764481/downloading-png-from-shiny-r
  # This function is used to plot and to downoad a pdf

  plotBox <- function(){
    cat(file = stderr(), 'plotBox\n')
    
    loc.dt = data4boxPlot()
    
    cat(file=stderr(), "plotBox: on to plot\n\n")
    if (is.null(loc.dt)) {
      cat(file=stderr(), 'plotBox: dt is NULL\n')
      return(NULL)
    }
    
    cat(file=stderr(), 'plotBox:dt not NULL\n')
    
    ggplot(loc.dt, aes(x = as.factor(realtime), y = y)) +
      geom_boxplot(aes(fill = group), 
                   #position = position_dodge(width = 1), 
                   notch = input$inPlotBoxNotches, 
                   outlier.colour = ifelse(input$inPlotBoxOutliers, 'red', NA)) + 
      scale_fill_discrete(name = '') +
      xlab('\nTime (min)') +
      ylab('') +
      theme_bw(base_size = 18, base_family = "Helvetica") +
      theme(
        panel.grid.minor = element_blank(),
        panel.grid.major = element_blank(),
        panel.border = element_blank(),
        axis.line.x = element_line(color = "black", size = 0.25),
        axis.line.y = element_line(color = "black", size = 0.25),
        axis.text.x = element_text(size = 12),
        axis.text.y = element_text(size = 12),
        strip.text.x = element_text(size = 14, face = "bold"),
        strip.text.y = element_text(size = 14, face = "bold"),
        strip.background = element_blank(),
        legend.key = element_blank(),
        legend.key.height = unit(1, "lines"),
        legend.key.width = unit(2, "lines"),
        legend.position = input$selPlotBoxLegendPos
      )
  }
dmattek's avatar
dmattek committed
543
})