trajRibbonPlot.R 10.6 KB
Newer Older
dmattek's avatar
dmattek committed
1
2
3
4
5
6
7
#
# Time Course Inspector: Shiny app for plotting time series data
# Author: Maciej Dobrzynski
#
# This module is for plotting group averages as ribbon plots (mean + 95%CI)
#

dmattek's avatar
dmattek committed
8
9
10
11
12
13
14

modTrajRibbonPlotUI =  function(id, label = "Plot Individual Time Series") {
  ns <- NS(id)
  
  tagList(
    fluidRow(
      column(
dmattek's avatar
dmattek committed
15
16
        3,
        radioButtons(ns('rBlegendPos'), 'Legend', list('top' = 'top', 'right' = 'right')),
17
        checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
dmattek's avatar
dmattek committed
18
19
        actionButton(ns('butPlotTraj'), 'Plot!')
      ),
20
21
      column(
        2,
dmattek's avatar
dmattek committed
22
        radioButtons(ns('rBPlotTrajStat'), 'Display', list('Mean only' = 'Mean',
23
24
25
                                                            'Add 95% CI' = 'CI', 
                                                            'Add SE' = 'SE'))
      ),
dmattek's avatar
dmattek committed
26
27
      column(
        3,
dmattek's avatar
dmattek committed
28
        sliderInput(ns('sliPlotTrajSkip'), 'Plot every n-th point', min = 1, max = 10, value = 1, step = 1),
dmattek's avatar
dmattek committed
29
        
dmattek's avatar
dmattek committed
30
        checkboxInput(ns('chBsetXbounds'), 'Bounds for X', FALSE),
dmattek's avatar
dmattek committed
31
32
33
34
35
36
37
38
        fluidRow(
          column(6,
                 uiOutput(ns('uiSetXboundsLow'))
          ),
          column(6,
                 uiOutput(ns('uiSetXboundsHigh'))
          )),
        
dmattek's avatar
dmattek committed
39
        checkboxInput(ns('chBsetYbounds'), 'Bounds for Y', FALSE),
dmattek's avatar
dmattek committed
40
41
42
43
44
45
46
        fluidRow(
          column(6,
                 uiOutput(ns('uiSetYboundsLow'))
          ),
          column(6,
                 uiOutput(ns('uiSetYboundsHigh'))
          ))
dmattek's avatar
dmattek committed
47
48
      ),
      column(
Maciej Dobrzynski's avatar
Maciej Dobrzynski committed
49
        2,
dmattek's avatar
dmattek committed
50
51
        numericInput(
          ns('inPlotTrajWidth'),
dmattek's avatar
dmattek committed
52
          'Width [%]',
Maciej Dobrzynski's avatar
Maciej Dobrzynski committed
53
          value = PLOTWIDTH,
dmattek's avatar
dmattek committed
54
55
56
57
58
59
          min = 10,
          width = '100px',
          step = 10
        ),
        numericInput(
          ns('inPlotTrajHeight'),
dmattek's avatar
dmattek committed
60
          'Height [px]',
Maciej Dobrzynski's avatar
Maciej Dobrzynski committed
61
          value = PLOTRIBBONHEIGHT,
dmattek's avatar
dmattek committed
62
63
64
65
66
67
68
69
70
          min = 100,
          width = '100px',
          step = 50
        )
      )
    ),
    uiOutput(ns('uiPlotTraj')),
    br(),
    modTrackStatsUI(ns('dispTrackStats')),
71
    br(),
dmattek's avatar
dmattek committed
72
    downPlotUI(ns('downPlotTraj'), "Download Plot")
dmattek's avatar
dmattek committed
73
74
75
76
  )
}


77
78
modTrajRibbonPlot = function(input, output, session, 
                             in.data, 
79
                             in.data.stim,
80
81
                             in.facet = 'group', 
                             in.facet.color = NULL, 
82
                             in.fname) {
dmattek's avatar
dmattek committed
83
84
85
  
  ns <- session$ns
  
dmattek's avatar
dmattek committed
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
  
  # UI for bounding the x-axis ====
  output$uiSetXboundsLow = renderUI({
    ns <- session$ns
    
    if(input$chBsetXbounds) {
      
      loc.dt = in.data()
      
      if (is.null(loc.dt)) {
        cat(file = stderr(), 'uiSetXboundsLow: dt is NULL\n')
        return(NULL)
      }
      
      numericInput(
        ns('inSetXboundsLow'),
        label = 'Lower',
        step = 0.1, 
        value = floor(min(loc.dt[[COLRT]], na.rm = T))
      )
    }
  })
  
  
  output$uiSetXboundsHigh = renderUI({
    ns <- session$ns
    
    if(input$chBsetXbounds) {
      
      loc.dt = in.data()
      
      if (is.null(loc.dt)) {
        cat(file = stderr(), 'uiSetXboundsHigh: dt is NULL\n')
        return(NULL)
      }
      
      numericInput(
        ns('inSetXboundsHigh'),
        label = 'Upper',
        step = 0.1, 
        value = ceil(max(loc.dt[[COLRT]], na.rm = T))
      )
    }
  })
  
  
  # UI for bounding the y-axis ====
  output$uiSetYboundsLow = renderUI({
    ns <- session$ns
    
    if(input$chBsetYbounds) {
      
      loc.dt = in.data()
      
      if (is.null(loc.dt)) {
        cat(file = stderr(), 'uiSetYboundsLow: dt is NULL\n')
        return(NULL)
      }
      
      numericInput(
        ns('inSetYboundsLow'),
        label = 'Lower',
        step = 0.1, 
dmattek's avatar
dmattek committed
149
        value = min(loc.dt[[COLY]], na.rm = T)
dmattek's avatar
dmattek committed
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
      )
    }
  })
  
  
  output$uiSetYboundsHigh = renderUI({
    ns <- session$ns
    
    if(input$chBsetYbounds) {
      
      loc.dt = in.data()
      
      if (is.null(loc.dt)) {
        cat(file = stderr(), 'uiSetYboundsHigh: dt is NULL\n')
        return(NULL)
      }
      
      numericInput(
        ns('inSetYboundsHigh'),
        label = 'Upper',
        step = 0.1, 
dmattek's avatar
dmattek committed
171
        value = max(loc.dt[[COLY]], na.rm = T)
dmattek's avatar
dmattek committed
172
173
174
175
176
177
      )
    }
  })
  
  # Plotting ====
  
dmattek's avatar
dmattek committed
178
179
  output$uiPlotTraj = renderUI({
    if (input$chBplotTrajInt)
180
181
182
183
184
       plotlyOutput(
       ns("outPlotTrajInt"),
       width = paste0(input$inPlotTrajWidth, '%'),
       height = paste0(input$inPlotTrajHeight, 'px')
    ) else
dmattek's avatar
dmattek committed
185
186
187
188
189
190
191
192
193
        plotOutput(
          ns("outPlotTraj"),
          width = paste0(input$inPlotTrajWidth, '%'),
          height = paste0(input$inPlotTrajHeight, 'px')
        )
  })
  
  
  callModule(modTrackStats, 'dispTrackStats',
dmattek's avatar
dmattek committed
194
195
             in.data = in.data,
             in.bycols = in.facet)
dmattek's avatar
dmattek committed
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
  
  
  output$outPlotTraj <- renderPlot({
    
    loc.p = plotTraj()
    if(is.null(loc.p))
      return(NULL)
    
    return(loc.p)
  })
  
  
  output$outPlotTrajInt <- renderPlotly({
    # 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
    if (names(dev.cur()) != "null device")
      dev.off()
    pdf(NULL)
    
    loc.p = plotTraj()
    if(is.null(loc.p))
      return(NULL)
    
    return(plotly_build(loc.p))
  })
  
  
  
  # Trajectory plot - download pdf
227
228
229
  callModule(downPlot, "downPlotTraj", 
             in.fname = in.fname, 
             plotTraj, TRUE)
dmattek's avatar
dmattek committed
230
231
  
  plotTraj <- function() {
232
    cat(file = stderr(), 'plotTrajRibbon: in\n')
dmattek's avatar
dmattek committed
233
234
    locBut = input$butPlotTraj
    
235
236
237
    # Check if main data exists
    # Thanks to solate all mods in the left panel are delayed 
    # until clicking the Plot button
dmattek's avatar
dmattek committed
238
    loc.dt = isolate(in.data())
239
240
241
    validate(
      need(!is.null(loc.dt), "Nothing to plot. Load data first!")
    )    
dmattek's avatar
dmattek committed
242
    
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
    cat(file = stderr(), 'plotTrajRibbon: dt not NULL\n')
    
    # check if stim data exists
    loc.dt.stim = isolate(in.data.stim())
    
    if (is.null(loc.dt.stim)) {
      cat(file = stderr(), 'plotTrajRibbon: stim is NULL\n')
    } else {
      cat(file = stderr(), 'plotTrajRibbon: stim not NULL\n')
      
      # choose only 1st group of stimulation pattern for ribbon plot
      
      loc.groups = unique(loc.dt.stim[['group']])
      if(length(loc.groups) > 1) {
        cat(file = stderr(), 'plotTrajRibbon: more than 1 group in stim; choosing 1st\n')
        loc.dt.stim = loc.dt.stim[group == loc.groups[1]]
      }
    }
    
dmattek's avatar
dmattek committed
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
    
    
    # Future: change such that a column with colouring status is chosen by the user
    # colour trajectories, if dataset contains mid.in 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
    
    # select every other point for plotting
    loc.dt = loc.dt[, .SD[seq(1, .N, input$sliPlotTrajSkip)], by = id]
    
    # check if columns with XY positions are present
    if (sum(names(loc.dt) %like% 'pos') == 2)
      locPos = TRUE
    else
      locPos = FALSE
    
    # check if column with ObjectNumber is present
    if (sum(names(loc.dt) %like% 'obj.num') == 1)
      locObjNum = TRUE
    else
      locObjNum = FALSE
    
    
    
    # If in.facet.color present,
    # make sure to include the same number of colours in the palette,
    # as the number of groups in dt.
    # in.facet.color is typically used when plotting time series within clusters.
    # Then, the number of colours in the palette has to be equal to the number of clusters (facetted according to in.facet variable).
    # This might differ if the user selects manually clusters to display.
    if (is.null(in.facet.color)) 
      loc.facet.col = NULL 
    else {
      # get group numbers in dt; 
      # loc.dt[, c(in.facet), with = FALSE] returns a data table with a single column
      # [[1]] at the end extracts the first column and returns as a vector
      loc.groups = unique(loc.dt[, c(in.facet), with = FALSE][[1]])
      
      # get colour palette
      # the length is equal to the number of groups in the original dt.
      # When plotting time series within clusters, the length equals the number of clusters.
      loc.facet.col = in.facet.color()$cl.col
      loc.facet.col = loc.facet.col[loc.groups]
    }
    
310
311
312
313
314
315
    
    # aggregate data; calculate Mean, CI or SE
    loc.ribbon.lohi = NULL
    
    if(input$rBPlotTrajStat == "Mean") {
      # calculate the mean
dmattek's avatar
dmattek committed
316
      loc.dt.aggr = loc.dt[, .(Mean = mean(get(COLY), na.rm = T)), by = c(in.facet, COLRT)]
317
318
319
320
321
322
323
324
325
326
327
328
      
    } else if(input$rBPlotTrajStat == "CI") {
      # calculate the mean and the confidence intervals
      loc.dt.aggr = LOCcalcTrajCI(in.dt = loc.dt, 
                                  in.col.meas = COLY, 
                                  in.col.by = c(in.facet, COLRT), 
                                  in.type = 'normal')
      
      loc.ribbon.lohi = c('Lower', 'Upper')
      
    } else if(input$rBPlotTrajStat == "SE") {
      # calculate the mean and the standard error of the mean
dmattek's avatar
dmattek committed
329
330
331
332
      loc.dt.aggr = loc.dt[, .(Mean = mean(get(COLY), na.rm = T),
                               Lower = mean(get(COLY), na.rm = T) - LOCstderr(get(COLY), na.rm = T),
                               Upper = mean(get(COLY), na.rm = T) + LOCstderr(get(COLY), na.rm = T)), 
                           by = c(in.facet, COLRT)]
333
334
335
336
337
338
339
      
      loc.ribbon.lohi = c('Lower', 'Upper')
    }
    
    
    
    # set the grouing column to a factor (for plotting)
dmattek's avatar
dmattek committed
340
341
    loc.dt.aggr[, (in.facet) := as.factor(get(in.facet))]

342
    # setting bounds for displaying of x and y axes
dmattek's avatar
dmattek committed
343
344
345
346
347
348
349
350
351
    loc.xlim.arg = NULL
    if(input$chBsetXbounds) {
      loc.xlim.arg = c(input$inSetXboundsLow, input$inSetXboundsHigh)
    } 
    
    loc.ylim.arg = NULL
    if(input$chBsetYbounds) {
      loc.ylim.arg = c(input$inSetYboundsLow, input$inSetYboundsHigh)
    } 
dmattek's avatar
dmattek committed
352
    
353
    p.out = LOCplotTrajRibbon(dt.arg = loc.dt.aggr, 
354
                           x.arg = COLRT, 
dmattek's avatar
dmattek committed
355
356
357
                           y.arg = 'Mean',
                           col.arg = loc.facet.col,
                           group.arg = in.facet,
358
359
                           dt.stim.arg = loc.dt.stim,
                           x.stim.arg = c('tstart', 'tend'),
360
361
                           y.stim.arg = c('ystart', 'yend'), 
                           ribbon.lohi.arg = loc.ribbon.lohi,
dmattek's avatar
dmattek committed
362
363
                           xlim.arg = loc.xlim.arg,
                           ylim.arg = loc.ylim.arg,
364
                           xlab.arg = 'Time',
365
                           ylab.arg = '') +
366
367
368
369
370
      LOCggplotTheme(in.font.base = PLOTFONTBASE, 
                     in.font.axis.text = PLOTFONTAXISTEXT, 
                     in.font.axis.title = PLOTFONTAXISTITLE, 
                     in.font.strip = PLOTFONTFACETSTRIP, 
                     in.font.legend = PLOTFONTLEGEND) + 
371
      theme(legend.position = input$rBlegendPos)
dmattek's avatar
dmattek committed
372
373
374
375
    
    return(p.out)
  }
}