In order to mitigate against the brute force attacks against Gitlab accounts, we are moving to all edu-ID Logins. We would like to remind you to link your account with your edu-id. Login will be possible only by edu-ID after November 30, 2021. Here you can find the instructions for linking your account.

If you don't have a SWITCH edu-ID, you can create one with this guide here

kind regards

This Server has been upgraded to GitLab release 14.2.6

ui.R 4.63 KB
Newer Older
dmattek's avatar
dmattek committed
1
#
dmattek's avatar
dmattek committed
2
3
# Time Course Inspector: Shiny app for plotting time series data
# Author: Maciej Dobrzynski
dmattek's avatar
dmattek committed
4
#
dmattek's avatar
dmattek committed
5
6
7
# This is the user-interface definition for a Shiny web application.
#

dmattek's avatar
dmattek committed
8
9

library(shiny)
dmattek's avatar
dmattek committed
10
library(shinyjs) #http://deanattali.com/shinyjs/
11
library(shinyBS)
dmattek's avatar
dmattek committed
12
13

shinyUI(fluidPage(
dmattek's avatar
dmattek committed
14
15
  useShinyjs(),
  # Include shinyjs
dmattek's avatar
dmattek committed
16
17
18
19
  
  # Application title
  title = "Timecourse Inspector",
  
dmattek's avatar
dmattek committed
20
21
22
23
24
  sidebarLayout(
    sidebarPanel(
      #Selector for file upload
      fileInput(
        'inFileLoadNuc',
25
        'Select main data file and press "Load Data"',
dmattek's avatar
dmattek committed
26
27
28
29
        accept = c('text/csv', 'text/comma-separated-values,text/plain')
      ),
      actionButton("inButLoadNuc", "Load Data"),
      actionButton("butReset", "Reset file input"),
30
      actionButton('inDataGen1', 'Synthetic data'),
dmattek's avatar
Added:    
dmattek committed
31
32
33
      
      tags$hr(),
      checkboxInput('chBtrajRem', 'Upload IDs to remove'),
34
      bsTooltip('chBtrajRem', help.text.short[1], placement = "right", trigger = "hover", options = NULL),
dmattek's avatar
Added:    
dmattek committed
35
36
37
38
      
      uiOutput('uiFileLoadTrajRem'),
      uiOutput('uiButLoadTrajRem'),
      
39
      #tags$hr(),
40
      checkboxInput('chBstim', 'Upload stimulation pattern'),
41
      bsTooltip('chBstim', help.text.short[4], placement = "right", trigger = "hover", options = NULL),
42
43
44
45
      
      uiOutput('uiFileLoadStim'),
      uiOutput('uiButLoadStim'),
      
46
47
48
      #tags$hr(),
      checkboxInput('chBtrajInter', 'Interpolate NAs and missing data', value = F),
      bsTooltip('chBtrajInter', help.text.short[3], placement = "right", trigger = "hover", options = NULL),
49
50
      
      uiOutput('varSelTimeFreq'),
51
52
53
54
55
56

      checkboxInput('chBtrackUni', 'Create unique track ID', F),
      bsTooltip('chBtrackUni', help.text.short[2], placement = "right", trigger = "hover", options = NULL),
      
      tags$hr(),

dmattek's avatar
dmattek committed
57
58
      uiOutput('varSelSite'),
      uiOutput('varSelTrackLabel'),
59
      
60
61
62
      checkboxInput('chBgroup', 'Select grouping column', F),                
      bsTooltip('chBgroup', help.text.short[5], placement = "right", trigger = "hover", options = NULL),

dmattek's avatar
dmattek committed
63
64
65
66
      uiOutput('varSelGroup'),
      uiOutput('varSelTime'),
      uiOutput('varSelMeas1'),
      radioButtons(
Maciej Dobrzynski's avatar
Maciej Dobrzynski committed
67
        'inSelMath', width = '50%',
68
        'Math on 1st and 2nd meas.:',
dmattek's avatar
dmattek committed
69
70
71
72
73
74
75
76
77
        c(
          'None' = '',
          'Divide' = " / ",
          'Sum' = " + ",
          'Multiply' = " * ",
          'Subtract' = ' - ',
          '1 / X' = '1 / '
        )
      ),
78
79
      bsTooltip('inSelMath', help.text.short[6], placement = "right", trigger = "hover", options = NULL),
      
dmattek's avatar
dmattek committed
80
81
      uiOutput('varSelMeas2'),
      
dmattek's avatar
dmattek committed
82
83
      tags$hr(),
      checkboxInput('chBtimeTrim', 'Trim x-axis', FALSE),
84
      bsTooltip('chBtimeTrim', help.text.short[7], placement = "right", trigger = "hover", options = NULL),
dmattek's avatar
dmattek committed
85
      uiOutput('uiSlTimeTrim'),
86

dmattek's avatar
dmattek committed
87
      checkboxInput('chBnorm', 'Normalization', FALSE),
88
      bsTooltip('chBnorm', help.text.short[8], placement = "right", trigger = "hover", options = NULL),
dmattek's avatar
dmattek committed
89
90
91
      uiOutput('uiChBnorm'),
      uiOutput('uiSlNorm'),
      uiOutput('uiChBnormRobust'),
dmattek's avatar
dmattek committed
92
      uiOutput('uiChBnormGroup'),
93

dmattek's avatar
dmattek committed
94
      tags$hr(),
95
96
      downloadButton('downloadDataClean', 'Download mod\'d data'),
      bsTooltip('downloadDataClean', help.text.short[9], placement = "right", trigger = "hover", options = NULL)
97
    ),
dmattek's avatar
dmattek committed
98
    
99
100
101
102
103
104
105
106
    mainPanel(
      tabsetPanel(
        tabPanel(
          "Time series",
          h4(
            "Plot time series: means per group or individual"
          ),
          br(),
dmattek's avatar
dmattek committed
107
          modSelOutliersUI('returnOutlierIDs'),
108
109
110
111
112
113
114
115
116
          tabsetPanel(
            tabPanel("Means",
                     br(),
                     modTrajRibbonPlotUI('modTrajRibbon')
            ),
            
            tabPanel(
              "Individual",
              br(),
117
              checkboxInput('chBhighlightTraj', 'Highlight trajectories', FALSE),
118
119
120
              uiOutput('varSelHighlight'),
              br(),
              modTrajPlotUI('modTrajPlot')
121
122
123
124
125
126
            ),
            
            tabPanel(
              "Power Spectral Density",
              br(),
              modPSDPlotUI('modPSDPlot')
127
128
            )
          )
dmattek's avatar
Added:    
dmattek committed
129
        ),
dmattek's avatar
Added:    
dmattek committed
130
        
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
        tabPanel(
          "AUC",
          modAUCplotUI('tabAUC')
        ),
        
        tabPanel(
          "Box-plots",
          tabBoxPlotUI('tabBoxPlot')
        ),
        
        
        # scatter plot
        tabPanel(
          'Scatter',
          tabScatterPlotUI('tabScatter')
        ),
        
        tabPanel(
          'Hierarchical',
          clustHierUI('tabClHier')
dmattek's avatar
dmattek committed
151
        ),
152
153
        
        # sparse hierarchical clustering package sparcl temporarily unavailable from CRAN
dmattek's avatar
dmattek committed
154
155
156
157
         tabPanel(
           'Hierarchical Sparse',
           clustHierSparUI('tabClHierSpar')
        )
158
      ))
dmattek's avatar
dmattek committed
159
160
  )
))