Changes in the UI, shinyBS help tips, added data distribution plot in outlier selection.

README.md

@@ -11,6 +11,7 @@ Following packages need to be installed in order to run the app locally:
 
 * shiny
 * shinyjs
+* shinybs
 * data.table
 * DT
 * ggplot2
@@ -31,7 +32,7 @@ Following packages need to be installed in order to run the app locally:
 Install packages using `install.packages('name_of_the_package_from_the_list_above')` command in RStudio command line.
 
 ```
-install.packages(c("shiny", "shinyjs", 
+install.packages(c("shiny", "shinyjs", "shinybs",
 					"data.table", "DT",
 					"ggplot2", "gplots", "plotly", "scales", "grid",
 					"dendextend", "RColorBrewer",

modules/auxfunc.R

@@ -19,11 +19,11 @@ require(Hmisc) # for CI calculation
 DEB = T
 
 # font sizes in pts for plots
-PLOTFONTBASE = 12
-PLOTFONTAXISTEXT = 12
-PLOTFONTAXISTITLE = 12
-PLOTFONTFACETSTRIP = 14
-PLOTFONTLEGEND = 12
+PLOTFONTBASE = 8
+PLOTFONTAXISTEXT = 8
+PLOTFONTAXISTITLE = 8
+PLOTFONTFACETSTRIP = 10
+PLOTFONTLEGEND = 8
 
 # default number of facets in plots
 PLOTNFACETDEFAULT = 3
@@ -152,6 +152,18 @@ help.text = c(
   'Accepts CSV file with 5 columns: grouping (e.g. condition), start and end time points of stimulation, start and end points of y-position, dummy column with id.'
 )
 
+help.text.short = c(
+  'Load CSV file with a column of cell IDs for removal. IDs should correspond to those used for plotting.',
+  'If the track ID is unique only within a group, make it unique globally by combining with the grouping column.',
+  'Interpolate missing tpts and pre-existing NAs. When checked, the interval of time column must be provided!',
+  'Load CSV file with 5 columns: grouping, start and end tpts of stimulation, start and end of y-position, dummy column with id.',
+  'Select columns to group data according to treatment, condition, etc.',
+  'Select math operation to perform on a single or two columns,',
+  'Select range of time for further processing.',
+  'Normalise data to a selected region.',
+  'Download data after modification in this section.'
+)
+
 # Functions for data processing ----
 #' Calculate the mean and CI around time series
 #'

modules/boxPlot.R

@@ -16,7 +16,7 @@ modBoxPlotUI =  function(id, label = "Plot Box-plots") {
                                                                 'Violin-plot' = 'viol',
                                                                 'Box-plot' = 'box', 
                                                                 'Line-plot' = 'line'), selected = 'box'),
-        checkboxInput(ns('chBPlotBoxInt'), 'Interactive Plot?'),
+        checkboxInput(ns('chBPlotBoxInt'), 'Interactive Plot'),
         actionButton(ns('butPlotBox'), 'Plot!')
       ),
       column(
@@ -85,7 +85,7 @@ modBoxPlot = function(input, output, session,
     ns <- session$ns
     
     if('box' %in% input$inPlotType)
-      checkboxInput(ns('inPlotBoxNotches'), 'Box plot notches?', FALSE)
+      checkboxInput(ns('inPlotBoxNotches'), 'Box plot notches', FALSE)
   })
   
   output$uiPlotBoxOutliers = renderUI({
@@ -94,7 +94,7 @@ modBoxPlot = function(input, output, session,
     ns <- session$ns
     
     if('box' %in% input$inPlotType)
-      checkboxInput(ns('inPlotBoxOutliers'), 'Box plot outliers?', FALSE)
+      checkboxInput(ns('inPlotBoxOutliers'), 'Box plot outliers', FALSE)
   })
   
   output$uiPlotBoxDodge = renderUI({

modules/selOutliers.R

@@ -21,7 +21,7 @@ modSelOutliersUI = function(id, label = "Outlier Selection") {
                          max = 100,
                          value = 0, 
                          step = 0.05, width = '100px'),
-             checkboxInput(ns('chBtrajInter'), 'Interpolate gaps?', value = F)
+             checkboxInput(ns('chBtrajInter'), 'Interpolate gaps', value = F)
       ),
       column(2, 
              radioButtons(ns('rbOutliersType'), 
@@ -40,7 +40,9 @@ modSelOutliersUI = function(id, label = "Outlier Selection") {
              downloadButton(ns('downOutlierCSV'), label = 'CSV with outlier IDs'),
              htmlOutput(ns("txtOutliersPerc"))
       )
-    )
+    ),
+    checkboxInput(ns('chBplotDist'), 'Plot data distribution', value = F),
+    uiOutput(ns('uiDistPlot'))
   )
 }
 
@@ -84,6 +86,117 @@ modSelOutliers = function(input, output, session, in.data) {
     }
   )
   
+  # Plot of value distribution
+  output$uiDistPlot <- renderUI({
+    ns <- session$ns
+    
+    if (input$chBplotDist) {
+
+      locDT = in.data()
+      
+      if (is.null(locDT)) {
+        return(NULL)
+      }
+
+      output$densPlot = renderPlot({
+
+        # main density plot
+        locP = ggplot(locDT, aes_string(x = COLY)) +
+          geom_density()
+        
+        # Shade regions of the density plot according to
+        # value set in input$numOutliersPerc.
+        
+        # extract data from density plot
+        locDTtmp = as.data.table(ggplot_build(locP)$data[[1]])
+        
+        # shade region on the right
+        if (input$rbOutliersType == 'top') {
+          
+          # find position of the right boundary
+          locQuantR = quantile(locDT[[COLY]], 
+                               1 - input$numOutliersPerc * 0.01, 
+                               na.rm = T, 
+                               type = 3)
+          
+          # select only those points of the density plot right to the right boundary
+          locDTtmpSub = locDTtmp[x > locQuantR]
+          
+          # add shaded RIGHT region to the plot
+          if (nrow(locDTtmpSub) > 0 )
+            locP = locP + 
+            geom_area(data = locDTtmpSub, aes(x=x, y=y), fill="red") +
+            geom_vline(xintercept = locQuantR, linetype = 'dashed', color = 'red')
+        } else 
+          # shade region on the left
+          if (input$rbOutliersType == 'bot') {
+            
+            # find position of the right boundary
+            locQuantL = quantile(locDT[[COLY]], 
+                                 input$numOutliersPerc * 0.01, 
+                                 na.rm = T, 
+                                 type = 3)
+            
+            # select only those points of the density plot left to the left boundary
+            locDTtmpSub = locDTtmp[x < locQuantL]
+            
+            # add shaded LEFT region to the plot
+            if (nrow(locDTtmpSub) > 0 )
+              locP = locP + 
+              geom_area(data = locDTtmpSub, aes(x=x, y=y), fill="red") +
+              geom_vline(xintercept = locQuantL, linetype = 'dashed', color = 'red')
+            
+          } else 
+            # shade region on the left
+            if (input$rbOutliersType == 'mid') {
+              
+              # find position of the right boundary
+              locQuantR = quantile(locDT[[COLY]], 
+                                   1 - input$numOutliersPerc * 0.005, 
+                                   na.rm = T, 
+                                   type = 3)
+              
+              # find position of the left boundary
+              locQuantL = quantile(locDT[[COLY]], 
+                                   input$numOutliersPerc * 0.005, 
+                                   na.rm = T, 
+                                   type = 3)
+              
+              # select only those points of the density plot left or right of the boundaries
+              locDTtmpSubL = locDTtmp[x < locQuantL]
+              locDTtmpSubR = locDTtmp[x > locQuantR]
+              
+              # add shaded LEFT region to the plot
+              if (nrow(locDTtmpSubL) > 0 )
+                locP = locP + 
+                geom_area(data = locDTtmpSubL, aes(x=x, y=y), fill="red") +
+                geom_vline(xintercept = locQuantL, linetype = 'dashed', color = 'red')
+              
+              
+              if (nrow(locDTtmpSubR) > 0 )
+                locP = locP + 
+                geom_area(data = locDTtmpSubR, aes(x=x, y=y), fill="red") +
+                geom_vline(xintercept = locQuantR, linetype = 'dashed', color = 'red')
+            }
+        
+        locP = locP +
+          xlab('Measurement value') +
+          LOCggplotTheme(in.font.base = PLOTFONTBASE, 
+                         in.font.axis.text = PLOTFONTAXISTEXT, 
+                         in.font.axis.title = PLOTFONTAXISTITLE, 
+                         in.font.strip = PLOTFONTFACETSTRIP, 
+                         in.font.legend = PLOTFONTLEGEND)
+        
+        return(locP)
+        
+      })
+      
+    } else
+      return(NULL)
+    
+    plotOutput(ns('densPlot'))
+  })
+  
 # Identify outliers and remove them from dt
   dtReturn = reactive({ 
     cat(file = stdout(), 'modSelOutliers: dtReturn\n')

modules/tabBoxPlot.R

@@ -3,7 +3,7 @@ tabBoxPlotUI =  function(id, label = "Comparing t-points") {
   
   tagList(
     h4(
-      "Box-/dot-/violin plot at selected time points"
+      "Box-/dot-/violin plot at selected t-points"
     ),
     br(),
     
@@ -99,7 +99,7 @@ tabBoxPlot = function(input, output, session, in.data, in.fname) {
     if (!is.null(loc.v)) {
       selectInput(
         ns('inSelTpts'),
-        'Select one or more timepoints:',
+        'Select one or more t-points:',
         loc.v,
         width = '100%',
         selected = 0,

modules/tabScatter.R

@@ -20,7 +20,7 @@ tabScatterPlotUI <- function(id, label = "Comparing t-points") {
   
   tagList(
     h4(
-      "Scatter plot between two time points"
+      "Scatter plot between two t-points"
     ),
     br(),
     
@@ -90,7 +90,7 @@ output$uiSelTptX = renderUI({
   if (!is.null(loc.v)) {
     selectInput(
       ns('inSelTptX'),
-      'Select timepoint for X-axis:',
+      'Select t-point for X-axis:',
       loc.v,
       width = '100%',
       selected = 0,
@@ -108,7 +108,7 @@ output$uiSelTptY = renderUI({
   if (!is.null(loc.v)) {
     selectInput(
       ns('inSelTptY'),
-      'Select timepoint for Y-axis:',
+      'Select t-point for Y-axis:',
       loc.v,
       width = '100%',
       selected = 0,

modules/trajPlot.R

@@ -25,7 +25,7 @@ modTrajPlotUI =  function(id, label = "Plot Individual Time Series") {
           width = '100px',
           step = 1
         ),
-        checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot?'),
+        checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
         actionButton(ns('butPlotTraj'), 'Plot!')
       ),
       column(
@@ -282,7 +282,7 @@ modTrajPlot = function(input, output, session,
       x.stim.arg = c('tstart', 'tend'),
       y.stim.arg = c('ystart', 'yend'), 
       stim.bar.width.arg = 1,
-      xlab.arg = 'Time (min)',
+      xlab.arg = 'Time',
       line.col.arg = loc.line.col.arg,
       aux.label1 = if (locPos) 'pos.x' else NULL,
       aux.label2 = if (locPos) 'pos.y' else NULL,

modules/trajRibbonPlot.R

@@ -7,7 +7,7 @@ modTrajRibbonPlotUI =  function(id, label = "Plot Individual Time Series") {
     fluidRow(
       column(
         3,
-        checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot?'),
+        checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
         radioButtons(ns('rBlegendPos'), 'Legend placement:', list('top' = 'top', 'right' = 'right')),
         actionButton(ns('butPlotTraj'), 'Plot!')
       ),
@@ -208,7 +208,7 @@ modTrajRibbonPlot = function(input, output, session,
                            dt.stim.arg = loc.dt.stim,
                            x.stim.arg = c('tstart', 'tend'),
                            y.stim.arg = c('ystart', 'yend'),
-                           xlab.arg = 'Time (min)',
+                           xlab.arg = 'Time',
                            ylab.arg = '') +
       LOCggplotTheme(in.font.base = PLOTFONTBASE, 
                      in.font.axis.text = PLOTFONTAXISTEXT, 

server.R

@@ -120,7 +120,7 @@ shinyServer(function(input, output, session) {
     if(input$chBtrajRem) 
       fileInput(
         'inFileLoadTrajRem',
-        'Select data file (e.g. badTraj.csv) and press "Load Data"',
+        'Select file and press "Load Data"',
         accept = c('text/csv', 'text/comma-separated-values,text/plain')
       )
   })
@@ -141,7 +141,7 @@ shinyServer(function(input, output, session) {
     if(input$chBstim) 
       fileInput(
         'inFileLoadStim',
-        'Select data file (e.g. stim.csv) and press "Load Data"',
+        'Select file and press "Load Data"',
         accept = c('text/csv', 'text/comma-separated-values,text/plain')
       )
   })
@@ -182,7 +182,7 @@ shinyServer(function(input, output, session) {
     
     selectInput(
       'inSelTime',
-      'Select time column (e.g. Metadata_T, RealTime):',
+      'Select time column:',
       locCols,
       width = '100%',
       selected = locColSel
@@ -196,7 +196,7 @@ shinyServer(function(input, output, session) {
     if (input$chBtrajInter) {
       numericInput(
         'inSelTimeFreq',
-        'Provide time frequency:',
+        'Frequency of time units:',
         min = 1,
         step = 1,
         width = '100%',
@@ -265,7 +265,7 @@ shinyServer(function(input, output, session) {
 
       selectInput(
         'inSelMeas1',
-        'Select 1st measurement:',
+        'Select 1st meas.:',
         locCols,
         width = '100%',
         selected = locColSel
@@ -286,7 +286,7 @@ shinyServer(function(input, output, session) {
 
       selectInput(
         'inSelMeas2',
-        'Select 2nd measurement',
+        'Select 2nd meas.',
         locCols,
         width = '100%',
         selected = locColSel

ui.R

@@ -8,6 +8,7 @@
 
 library(shiny)
 library(shinyjs) #http://deanattali.com/shinyjs/
+library(shinyBS)
 
 shinyUI(fluidPage(
   useShinyjs(),
@@ -21,65 +22,50 @@ shinyUI(fluidPage(
       #Selector for file upload
       fileInput(
         'inFileLoadNuc',
-        'Select data file (e.g. file.csv) and press "Load Data"',
+        'Select main data file and press "Load Data"',
         accept = c('text/csv', 'text/comma-separated-values,text/plain')
       ),
       actionButton("inButLoadNuc", "Load Data"),
       actionButton("butReset", "Reset file input"),
-      actionButton('inDataGen1', 'Generate artificial dataset'),
+      actionButton('inDataGen1', 'Synthetic data'),
       
       tags$hr(),
       checkboxInput('chBtrajRem', 'Upload IDs to remove'),
-      helpPopup(
-        title = 'Remove time series',
-        content = help.text[1],
-        placement = 'right',
-        trigger = 'hover'
-      ),
+      bsTooltip('chBtrajRem', help.text.short[1], placement = "right", trigger = "hover", options = NULL),
       
       uiOutput('uiFileLoadTrajRem'),
       uiOutput('uiButLoadTrajRem'),
       
-      tags$hr(),
+      #tags$hr(),
       checkboxInput('chBstim', 'Upload stimulation pattern'),
-      helpPopup(
-        title = 'Upload stimulations',
-        content = help.text[4],
-        placement = 'right',
-        trigger = 'hover'
-      ),
+      bsTooltip('chBstim', help.text.short[4], placement = "right", trigger = "hover", options = NULL),
       
       uiOutput('uiFileLoadStim'),
       uiOutput('uiButLoadStim'),
       
-      tags$hr(),
-      checkboxInput('chBtrajInter', 'Interpolate NAs and missing data?', value = F),
-      helpPopup(
-        title = 'Interpolation of NAs and missing data',
-        content = help.text[3],
-        placement = 'right',
-        trigger = 'hover'
-      ),
+      #tags$hr(),
+      checkboxInput('chBtrajInter', 'Interpolate NAs and missing data', value = F),
+      bsTooltip('chBtrajInter', help.text.short[3], placement = "right", trigger = "hover", options = NULL),
       
       uiOutput('varSelTimeFreq'),
-      checkboxInput('chBtrackUni', 'Create unique TrackLabel', F),
-      helpPopup(
-        title = 'Create unique cell ID',
-        content = help.text[2],
-        placement = 'right',
-        trigger = 'hover'
-      ),
+
+      checkboxInput('chBtrackUni', 'Create unique track ID', F),
+      bsTooltip('chBtrackUni', help.text.short[2], placement = "right", trigger = "hover", options = NULL),
+      
+      tags$hr(),
+
       uiOutput('varSelSite'),
       uiOutput('varSelTrackLabel'),
       
-      tags$hr(),
-      checkboxInput('chBgroup', 'Dataset contains grouping column (e.g. treatment, condition)', F),                
+      checkboxInput('chBgroup', 'Select grouping column', F),                
+      bsTooltip('chBgroup', help.text.short[5], placement = "right", trigger = "hover", options = NULL),
+
       uiOutput('varSelGroup'),
       uiOutput('varSelTime'),
       uiOutput('varSelMeas1'),
       radioButtons(
-        'inSelMath',
-        'Math operation 1st and 2nd meas.:',
+        'inSelMath', width = '25%',
+        'Math on 1st and 2nd meas.:',
         c(
           'None' = '',
           'Divide' = " / ",
@@ -89,19 +75,25 @@ shinyUI(fluidPage(
           '1 / X' = '1 / '
         )
       ),
+      bsTooltip('inSelMath', help.text.short[6], placement = "right", trigger = "hover", options = NULL),
+      
       uiOutput('varSelMeas2'),
       
       tags$hr(),
       checkboxInput('chBtimeTrim', 'Trim x-axis', FALSE),
+      bsTooltip('chBtimeTrim', help.text.short[7], placement = "right", trigger = "hover", options = NULL),
       uiOutput('uiSlTimeTrim'),
-      tags$hr(),
+
       checkboxInput('chBnorm', 'Normalization', FALSE),
+      bsTooltip('chBnorm', help.text.short[8], placement = "right", trigger = "hover", options = NULL),
       uiOutput('uiChBnorm'),
       uiOutput('uiSlNorm'),
       uiOutput('uiChBnormRobust'),
       uiOutput('uiChBnormGroup'),
+
       tags$hr(),
-      downloadButton('downloadDataClean', 'Download mod\'d data')
+      downloadButton('downloadDataClean', 'Download mod\'d data'),
+      bsTooltip('downloadDataClean', help.text.short[9], placement = "right", trigger = "hover", options = NULL)
     ),
     
     mainPanel(
@@ -122,7 +114,7 @@ shinyUI(fluidPage(
             tabPanel(
               "Individual",
               br(),
-              checkboxInput('chBhighlightTraj', 'Highlight trajectories?', FALSE),
+              checkboxInput('chBhighlightTraj', 'Highlight trajectories', FALSE),
               uiOutput('varSelHighlight'),
               br(),
               modTrajPlotUI('modTrajPlot')