tabClHier.R 14.3 KB
Newer Older
dmattek's avatar
Added:  
dmattek committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
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

# UI
clustHierUI <- function(id, label = "Hierarchical CLustering") {
  ns <- NS(id)
  
  tagList(
    br(),
    fluidRow(
      column(4,
             selectInput(
               ns("selectPlotHierLinkage"),
               label = ("Select linkage method:"),
               choices = list(
                 "Ward" = 1,
                 "Ward D2" = 2,
                 "Single" = 3,
                 "Complete" = 4,
                 "Average" = 5,
                 "McQuitty" = 6,
                 "Centroid" = 7
               ),
               selected = 2
             ),
             selectInput(
               ns("selectPlotHierDiss"),
               label = ("Select type of dissimilarity measure:"),
               choices = list("Euclidean" = 1,
                              "Maximum" = 2,
                              "Manhattan" = 3,
                              "Canberra" = 4,
                              "Binary" = 5,
                              "Minkowski" = 6,
                              "DTW" = 7),
               selected = 1
             )
      ),
      column(4,
             sliderInput(
               ns('inPlotHierNclust'),
               '#dendrogram branches to colour',
               min = 1,
               max = 20,
               value = 1,
               step = 1,
               ticks = TRUE,
               round = TRUE
             ),
             checkboxInput(ns('chBPlotHierClSel'), 'Manually select clusters to display'),
             uiOutput(ns('uiPlotHierClSel')),
             downloadButton(ns('downCellCl'), 'Download CSV with cell IDs and cluster no.')
      )
    ),
    
    br(),

    tabsetPanel(
      tabPanel('Heat-map',
               fluidRow(
                 column(3,
                        checkboxInput(ns('selectPlotHierDend'), 'Plot dendrogram and re-order samples', TRUE),
                        selectInput(
62
63
64
65
                          ns("selectPlotHierPaletteDend"),
                          label = "Dendrogram\'s colour palette:",
                          choices = l.col.pal.dend,
                          selected = 'Rainbow'
dmattek's avatar
Added:  
dmattek committed
66
                        ),
67

dmattek's avatar
Added:  
dmattek committed
68
69
70
                        checkboxInput(ns('selectPlotHierKey'), 'Plot colour key', TRUE)
                 ),
                 column(3,
71
72
73
74
75
76
77
                        selectInput(
                          ns("selectPlotHierPalette"),
                          label = "Heatmap\'s colour palette:",
                          choices = l.col.pal,
                          selected = 'Spectral'
                        ),
                        checkboxInput(ns('inPlotHierRevPalette'), 'Reverse heatmap\'s colour palette', TRUE),
dmattek's avatar
Added:  
dmattek committed
78
79
80
81
82
83
84
85
                        sliderInput(
                          ns('inPlotHierNAcolor'),
                          'Shade of grey for NA values (0 - black, 1 - white)',
                          min = 0,
                          max = 1,
                          value = 0.8,
                          step = .1,
                          ticks = TRUE
86
87
88
89
90
                        )
                 ),
                 column(6,
                        h4('Classic hierarchical clustering'),
                        br(),
dmattek's avatar
Added:  
dmattek committed
91
92
93
94
95
                        numericInput(ns('inPlotHierHeatMapHeight'), 
                                     'Display plot height [px]', 
                                     value = 600, 
                                     min = 100,
                                     step = 100)
96
                        
dmattek's avatar
Added:  
dmattek committed
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
                 )
               ),
               
               fluidRow(
                 column(
                   3,
                   numericInput(
                     ns('inPlotHierMarginX'),
                     'Margin below x-axis',
                     5,
                     min = 1,
                     width = 100
                   )
                 ),
                 column(
                   3,
                   numericInput(
                     ns('inPlotHierMarginY'),
                     'Margin right of y-axis',
                     20,
                     min = 1,
                     width = 100
                   )
                 ),
                 column(
                   3,
                   numericInput(
                     ns('inPlotHierFontX'),
                     'Font size row labels',
                     1,
                     min = 0,
                     width = 100,
                     step = 0.1
                   )
                 ),
                 column(
                   3,
                   numericInput(
                     ns('inPlotHierFontY'),
                     'Font size column labels',
                     1,
                     min = 0,
                     width = 100,
                     step = 0.1
                   )
                 )
               ),
               br(),
               
               downPlotUI(ns('downPlotHier'), "Download PDF"),
               actionButton(ns('butPlotHierHeatMap'), 'Plot!'),
               plotOutput(ns('outPlotHier'))
      ),

      tabPanel('Time-courses',
               modTrajPlotUI(ns('modPlotHierTraj'))),
      
dmattek's avatar
dmattek committed
154
155
156
      tabPanel('Averages',
               modTrajRibbonPlotUI(ns('modPlotHierTrajRibbon'))),
      
dmattek's avatar
Added:  
dmattek committed
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
      tabPanel('Cluster dist.',
               modClDistPlotUI(ns('hierClDistPlot'), 'xxx'))
      
    )
  )
}

# SERVER
clustHier <- function(input, output, session, in.data4clust, in.data4trajPlot) {
  
  output$uiPlotHierClSel = renderUI({
    ns <- session$ns
    
    if(input$chBPlotHierClSel) {
      selectInput(ns('inPlotHierClSel'), 'Select clusters to display', 
                  choices = seq(1, input$inPlotHierNclust, 1),
                  multiple = TRUE, 
                  selected = 1)
    }
  })
  
  # calculate distance matrix for further clustering
  # time series arranged in rows with columns corresponding to time points
  userFitDistHier <- reactive({
    cat(file = stderr(), 'userFitDistHier \n')
    
    dm.t = in.data4clust()

    if (is.null(dm.t)) {
      return(NULL)
    }
    
189
    #pr_DB$set_entry(FUN = fastDTW, names = c("fastDTW"))
dmattek's avatar
Added:  
dmattek committed
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
    cl.dist = dist(dm.t, method = s.cl.diss[as.numeric(input$selectPlotHierDiss)])
    
    return(cl.dist)
  })
  
  # perform hierarchical clustering and return dendrogram coloured according to cutree
  # branch coloring performed using dendextend package
  userFitDendHier <- reactive({
    cat(file = stderr(), 'userFitDendHier \n')
    
    dm.dist = userFitDistHier()
    
    if (is.null(dm.dist)) {
      return(NULL)
    }
    
    cl.hc = hclust(dm.dist, method = s.cl.linkage[as.numeric(input$selectPlotHierLinkage)])
207

dmattek's avatar
Added:  
dmattek committed
208
209
    dend <- as.dendrogram(cl.hc)
    dend <- color_branches(dend, 
210
                           col = get(input$selectPlotHierPaletteDend), # make sure that n here equals max in the input$inPlotHierNclust slider
dmattek's avatar
Added:  
dmattek committed
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
                           k = input$inPlotHierNclust)
    
    return(dend)
  })
  

  # returns table prepared with f-n getClCol
  # for hierarchical clustering
  getClColHier <- reactive({
    cat(file = stderr(), 'getClColHier \n')
    
    loc.dend = userFitDendHier()
    if (is.null(loc.dend))
      return(NULL)
    
226
227
228
229
230
231
232
233
234
235
236
    loc.dt = getClCol(loc.dend, input$inPlotHierNclust)
    
    # Display clusters specified in the inPlotHierClSel field
    # Data is ordered according to the order of clusters specified in this field
    if(input$chBPlotHierClSel) {
      loc.dt = loc.dt[cl.no %in% input$inPlotHierClSel]
      loc.dt[, cl.no := factor(cl.no, levels = input$inPlotHierClSel)]
      setkey(loc.dt, cl.no)
    }
    
    return(loc.dt)
dmattek's avatar
Added:  
dmattek committed
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
  })
  
  
  
  # return all unique track object labels (created in dataMod)
  # This will be used to display in UI for trajectory highlighting
  getDataTrackObjLabUni_afterTrim <- reactive({
    cat(file = stderr(), 'getDataTrackObjLabUni_afterTrim\n')
    loc.dt = in.data4trajPlot()
    
    if (is.null(loc.dt))
      return(NULL)
    else
      return(unique(loc.dt$id))
  })
  
  # return dt with cell IDs and their corresponding condition name
  # The condition is the column defined by facet groupings
  getDataCond <- reactive({
    cat(file = stderr(), 'getDataCond\n')
    loc.dt = in.data4trajPlot()
    
    if (is.null(loc.dt))
      return(NULL)
    else
      return(unique(loc.dt[, .(id, group)]))
    
  })
  
  # prepare data for plotting trajectories per cluster
  # outputs dt as data4trajPlot but with an additional column 'cl' that holds cluster numbers
  # additionally some clusters are omitted according to manual selection
  data4trajPlotCl <- reactive({
    cat(file = stderr(), 'data4trajPlotCl: in\n')
    
    loc.dt = in.data4trajPlot()
    
    if (is.null(loc.dt)) {
      cat(file = stderr(), 'data4trajPlotCl: dt is NULL\n')
      return(NULL)
    }
    
    cat(file = stderr(), 'data4trajPlotCl: dt not NULL\n')
    
    # get cellIDs with cluster assignments based on dendrogram cut
dmattek's avatar
dmattek committed
282
    loc.dt.cl = getDataCl(userFitDendHier(), input$inPlotHierNclust)
dmattek's avatar
Added:  
dmattek committed
283
284
    loc.dt = merge(loc.dt, loc.dt.cl, by = 'id')
    
285
286
287
    # Display clusters specified in the inPlotHierClSel field
    # Data is ordered according to the order of clusters specified in this field
    if(input$chBPlotHierClSel) {
dmattek's avatar
Added:  
dmattek committed
288
      loc.dt = loc.dt[cl %in% input$inPlotHierClSel]
289
290
291
      loc.dt[, cl := factor(cl, levels = input$inPlotHierClSel)]
      setkey(loc.dt, cl)
    }
dmattek's avatar
Added:  
dmattek committed
292
293
294
295
296
297
298
299
300
301
302
303
304
305
    
    return(loc.dt)    
  })
  
  # download a list of cellIDs with cluster assignments
  output$downCellCl <- downloadHandler(
    filename = function() {
      paste0('clust_hierch_data_',
             s.cl.diss[as.numeric(input$selectPlotHierDiss)],
             '_',
             s.cl.linkage[as.numeric(input$selectPlotHierLinkage)], '.csv')
    },
    
    content = function(file) {
dmattek's avatar
dmattek committed
306
      write.csv(x = getDataCl(userFitDendHier(), input$inPlotHierNclust), file = file, row.names = FALSE)
dmattek's avatar
Added:  
dmattek committed
307
308
309
310
311
312
313
314
315
316
317
318
319
320
    }
  )
  
  # prepare data for barplot with distribution of items per condition  
  data4clDistPlot <- reactive({
    cat(file = stderr(), 'data4clDistPlot: in\n')
    
    # get cell IDs with cluster assignments depending on dendrogram cut
    loc.dend <- userFitDendHier()
    if (is.null(loc.dend)) {
      cat(file = stderr(), 'plotClDist: loc.dend is NULL\n')
      return(NULL)
    }
    
dmattek's avatar
dmattek committed
321
322
    # get cell id's with associated cluster numbers
    loc.dt.cl = getDataCl(loc.dend, input$inPlotHierNclust)
dmattek's avatar
Added:  
dmattek committed
323
324
325
326
327
328
329
330
331
332
    
    # get cellIDs with condition name
    loc.dt.gr = getDataCond()
    if (is.null(loc.dt.gr)) {
      cat(file = stderr(), 'plotClDist: loc.dt.gr is NULL\n')
      return(NULL)
    }
    
    loc.dt = merge(loc.dt.cl, loc.dt.gr, by = 'id')
    
333
      
dmattek's avatar
Added:  
dmattek committed
334
335
    loc.dt.aggr = loc.dt[, .(nCells = .N), by = .(group, cl)]
    
336
337
338
339
340
341
342
    # Display clusters specified in the inPlotHierClSel field
    # Data is ordered according to the order of clusters specified in this field
    if(input$chBPlotHierClSel) {
      loc.dt.aggr = loc.dt.aggr[cl %in% input$inPlotHierClSel]
      loc.dt.aggr[, cl := factor(cl, levels = input$inPlotHierClSel)]
      setkey(loc.dt.aggr, cl)
    }
dmattek's avatar
Added:  
dmattek committed
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
    return(loc.dt.aggr)
    
  })
  
 
  # 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
  plotHier <- function() {
    
    loc.dm = in.data4clust()
    if (is.null(loc.dm))
      return(NULL)
    
    loc.dend <- userFitDendHier()
    if (is.null(loc.dend))
      return(NULL)
    
    loc.p = myPlotHeatmap(loc.dm,
                          loc.dend, 
                          palette.arg = input$selectPlotHierPalette, 
                          palette.rev.arg = input$inPlotHierRevPalette, 
                          dend.show.arg = input$selectPlotHierDend, 
                          key.show.arg = input$selectPlotHierKey, 
                          margin.x.arg = input$inPlotHierMarginX, 
                          margin.y.arg = input$inPlotHierMarginY, 
                          nacol.arg = input$inPlotHierNAcolor, 
                          font.row.arg = input$inPlotHierFontX, 
                          font.col.arg = input$inPlotHierFontY, 
                          title.arg = paste(
                            "Distance measure: ",
                            s.cl.diss[as.numeric(input$selectPlotHierDiss)],
                            "\nLinkage method: ",
                            s.cl.linkage[as.numeric(input$selectPlotHierLinkage)]
                          ))
    
    return(loc.p)
  }
  
  
   
  #  Hierarchical - display heatmap
  getPlotHierHeatMapHeight <- function() {
    return (input$inPlotHierHeatMapHeight)
  }
 
  output$outPlotHier <- renderPlot({
    locBut = input$butPlotHierHeatMap
    
    if (locBut == 0) {
      cat(file = stderr(), 'outPlotHier: Go button not pressed\n')
      
      return(NULL)
    }
    
    plotHier()
  }, height = getPlotHierHeatMapHeight)
  
  
  #  Hierarchical - Heat Map - download pdf
  callModule(downPlot, "downPlotHier",       paste0('clust_hierch_heatMap_',
                                                    s.cl.diss[as.numeric(input$selectPlotHierDiss)],
                                                    '_',
                                                    s.cl.linkage[as.numeric(input$selectPlotHierLinkage)], '.png'), plotHier)
  
  callModule(modTrajPlot, 'modPlotHierTraj', 
             in.data = data4trajPlotCl, 
             in.facet = 'cl',  
             in.facet.color = getClColHier,
             in.fname = paste0('clust_hierch_tCourses_',
                               s.cl.diss[as.numeric(input$selectPlotHierDiss)],
                               '_',
                               s.cl.linkage[as.numeric(input$selectPlotHierLinkage)], '.pdf'))
  
dmattek's avatar
dmattek committed
417
418
419
420
421
422
423
424
425
  callModule(modTrajRibbonPlot, 'modPlotHierTrajRibbon', 
             in.data = data4trajPlotCl, 
             in.facet = 'cl',  
             in.facet.color = getClColHier,
             in.fname = paste0('clust_hierch_tCoursesMeans_',
                               s.cl.diss[as.numeric(input$selectPlotHierDiss)],
                               '_',
                               s.cl.linkage[as.numeric(input$selectPlotHierLinkage)], '.pdf'))
  
dmattek's avatar
Added:  
dmattek committed
426
427
428
429
430
431
432
433
434
435
  callModule(modClDistPlot, 'hierClDistPlot', 
             in.data = data4clDistPlot,
             in.cols = getClColHier,
             in.fname = paste0('clust_hierch_clDist_',
                               s.cl.diss[as.numeric(input$selectPlotHierDiss)],
                               '_',
                               s.cl.linkage[as.numeric(input$selectPlotHierLinkage)], '.pdf'))

  
}