boxPlot.R 7.74 KB
Newer Older
dmattek's avatar
dmattek committed
1
2
3
4
5
#
# Time Course Inspector: Shiny app for plotting time series data
# Author: Maciej Dobrzynski
#
# This module is for plotting a choice of box/violin/dot-plots
dmattek's avatar
Added:  
dmattek committed
6
7
8
9
10
11
# Assumes in.data contains columns:
# realtime
# y
# group
# id

dmattek's avatar
dmattek committed
12
# UI ----
dmattek's avatar
Added:  
dmattek committed
13
14
15
16
17
18
19
20
21
22
23
modBoxPlotUI =  function(id, label = "Plot Box-plots") {
  ns <- NS(id)
  
  tagList(
    fluidRow(
      column(
        4,
        checkboxGroupInput(ns('inPlotType'), 'Plot type:', list('Dot-plot' = 'dot', 
                                                                'Violin-plot' = 'viol',
                                                                'Box-plot' = 'box', 
                                                                'Line-plot' = 'line'), selected = 'box'),
24
        checkboxInput(ns('chBPlotBoxInt'), 'Interactive Plot'),
dmattek's avatar
Added:  
dmattek committed
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
        actionButton(ns('butPlotBox'), 'Plot!')
      ),
      column(
        4,
        selectInput(
          ns('selPlotBoxLegendPos'),
          label = 'Select legend position',
          choices = list(
            "Top" = 'top',
            "Right" = 'right',
            "Bottom" = 'bottom'
          ),
          selected = 'top'
        ),
        uiOutput(ns('uiPlotBoxNotches')),
        uiOutput(ns('uiPlotBoxOutliers')),
        uiOutput(ns('uiPlotBoxDodge')),
        #uiOutput(ns('uiPlotBoxWidth')),
        uiOutput(ns('uiPlotBoxAlpha')),
        uiOutput(ns('uiPlotDotNbins'))
      ),
      column(
        4,
        numericInput(
          ns('inPlotBoxWidth'),
          'Width [%]:',
Maciej Dobrzynski's avatar
Maciej Dobrzynski committed
51
          value = PLOTWIDTH,
dmattek's avatar
Added:  
dmattek committed
52
53
54
55
56
57
58
          min = 10,
          width = '100px',
          step = 10
        ),
        numericInput(
          ns('inPlotBoxHeight'),
          'Height [px]:',
Maciej Dobrzynski's avatar
Maciej Dobrzynski committed
59
          value = PLOTBOXHEIGHT,
dmattek's avatar
Added:  
dmattek committed
60
61
62
          min = 100,
          width = '100px',
          step = 50
dmattek's avatar
dmattek committed
63
64
65
        ),
        radioButtons(ns("rBAxisLabelsRotate"), "X-axis labels:",
                     c("horizontal" = 0,
dmattek's avatar
dmattek committed
66
                       "45 deg" = 45,
dmattek's avatar
dmattek committed
67
                       "90 deg" = 90))
dmattek's avatar
Added:  
dmattek committed
68
69
70
71
72
73
74
75
      )
    ),
    
    uiOutput(ns('uiPlotBox')),
    downPlotUI(ns('downPlotBox'), "Download PDF")
  )
}

dmattek's avatar
dmattek committed
76
# SERVER ----
dmattek's avatar
Added:  
dmattek committed
77
78
79
80
81
82
modBoxPlot = function(input, output, session, 
                      in.data, 
                      in.cols = list(meas.x = 'realtime',
                                     meas.y = 'y',
                                     group = 'group',
                                     id = 'id'), 
83
                      in.fname) {
dmattek's avatar
Added:  
dmattek committed
84
85
86
87
88
89
90
91
92
  
  ns <- session$ns
 
  output$uiPlotBoxNotches = renderUI({
    cat(file = stderr(), 'UI uiPlotBoxNotches\n')
    
    ns <- session$ns
    
    if('box' %in% input$inPlotType)
93
      checkboxInput(ns('inPlotBoxNotches'), 'Box plot notches', FALSE)
dmattek's avatar
Added:  
dmattek committed
94
95
96
97
98
99
100
101
  })
  
  output$uiPlotBoxOutliers = renderUI({
    cat(file = stderr(), 'UI uiPlotBoxNotches\n')
    
    ns <- session$ns
    
    if('box' %in% input$inPlotType)
102
      checkboxInput(ns('inPlotBoxOutliers'), 'Box plot outliers', FALSE)
dmattek's avatar
Added:  
dmattek committed
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
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
  })
  
  output$uiPlotBoxDodge = renderUI({
    cat(file = stderr(), 'UI uiPlotBoxDodge\n')
    
    ns <- session$ns
    
    if(!( 'line' %in% input$inPlotType  ))
      sliderInput(ns('inPlotBoxDodge'), 'Dodge series:', min = 0, max = 1, value = .4, step = 0.05)
  })
  
  output$uiPlotBoxWidth = renderUI({
    cat(file = stderr(), 'UI uiPlotBoxWidth\n')
    
    ns <- session$ns
    
    if('box' %in% input$inPlotType)
      sliderInput(ns('inPlotBoxWidth'), 'Box plot width:', min = 0, max = 1, value = .2, step = 0.1)
  })
  
  output$uiPlotBoxAlpha = renderUI({
    cat(file = stderr(), 'UI uiPlotBoxAlpha\n')
    
    ns <- session$ns
    
    if('box' %in% input$inPlotType)
      sliderInput(ns('inPlotBoxAlpha'), 'Box plot transparency:', min = 0, max = 1, value = 1, step = 0.05)
  })
  
  output$uiPlotDotNbins = renderUI({
    cat(file = stderr(), 'UI uiPlotDotNbins\n')
    
    ns <- session$ns
    
    if('dot' %in% input$inPlotType)
      sliderInput(ns('inPlotDotNbins'), 'Dot-plot bin size (10^x):', min = -4, max = 4, value = -1.5, step = 0.1)
  })
  
  # Boxplot - display
  output$outPlotBox = renderPlot({
    locBut = input$butPlotBox
    
    if (locBut == 0) {
      cat(file = stderr(), 'plotBox: Go button not pressed\n')
      return(NULL)
    }
    
    plotBox()
    
  })
  
  
  output$outPlotBoxInt = renderPlotly({
    locBut = input$butPlotBox
    
    if (locBut == 0) {
      cat(file = stderr(), 'plotBox: Go button not pressed\n')
      return(NULL)
    }
    
    # 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)
    
    return( ggplotly(plotBox())  %>% layout(boxmode = 'group', width = '100%', height = '100%'))
    
  })
  
  
  output$uiPlotBox <- renderUI({
    ns <- session$ns
    
    if (input$chBPlotBoxInt)
      plotlyOutput(ns("outPlotBoxInt"), 
                   width = paste0(input$inPlotBoxWidth, '%'),
                   height = paste0(input$inPlotBoxHeight, 'px'))
    else
      plotOutput(ns('outPlotBox'),
                 width = paste0(input$inPlotBoxWidth, '%'),
                 height = paste0(input$inPlotBoxHeight, 'px'))
  })
  
  # Boxplot - download pdf
  callModule(downPlot, "downPlotBox", in.fname, plotBox, TRUE)
  
  # 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 = in.data()
    
    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')
    
    loc.par.dodge <- position_dodge(width = input$inPlotBoxDodge)
    p.out = ggplot(loc.dt, aes_string(x = sprintf("factor(%s)", in.cols[['meas.x']]), y = in.cols[['meas.y']])) 
    
    if('dot' %in% input$inPlotType)
      p.out = p.out + geom_dotplot(aes_string(fill = in.cols[['group']]), 
dmattek's avatar
dmattek committed
213
                                   color = NA,
dmattek's avatar
Added:  
dmattek committed
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
                                   binaxis = "y", 
                                   stackdir = "center", 
                                   position = loc.par.dodge, 
                                   binwidth = 10^(input$inPlotDotNbins), 
                                   method = 'histodot')
    
    if('viol' %in% input$inPlotType)
      p.out = p.out + geom_violin(aes_string(fill = in.cols[['group']]),
                                  position = loc.par.dodge,
                                  width = 0.2)
    
    if('line' %in% input$inPlotType)
      p.out = p.out + 
      geom_path(aes_string(color = in.cols[['group']], group = in.cols[['id']])) +
      facet_wrap(as.formula(paste("~", in.cols[['group']])))
    
    if ('box' %in% input$inPlotType)
      p.out = p.out + geom_boxplot(
        aes_string(fill = in.cols[['group']]), 
        position = loc.par.dodge,
        #width = 0.2, #input$inPlotBoxWidth,
        notch = input$inPlotBoxNotches, 
        alpha = input$inPlotBoxAlpha,
        outlier.colour = if (input$inPlotBoxOutliers)
          'red'
        else
          NA
      ) 
    
    p.out = p.out +
      scale_fill_discrete(name = '') +
      xlab('') +
      ylab('') +
247
248
249
250
251
      LOCggplotTheme(in.font.base = PLOTFONTBASE, 
                     in.font.axis.text = PLOTFONTAXISTEXT, 
                     in.font.axis.title = PLOTFONTAXISTITLE, 
                     in.font.strip = PLOTFONTFACETSTRIP, 
                     in.font.legend = PLOTFONTLEGEND) + 
dmattek's avatar
dmattek committed
252
      theme(legend.position = input$selPlotBoxLegendPos,
253
254
            axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate), 
                                                    size = PLOTFONTAXISTEXT))
dmattek's avatar
dmattek committed
255

dmattek's avatar
Added:  
dmattek committed
256
257
258
259
260
    
    return(p.out)
  }
  
}