Changes in help text

modules/auxfunc.R

@@ -177,8 +177,18 @@ helpPopup <- function(title, content,
 }
 
 helpText.server = c(
-  'Load main data as a CSV or compressed CSV file (gz or bz2).',                                                                   #1
-  'Long format: a row is a single data point. Wide format: a row is a time series with columns as time points.',                   #2
+  alDataFormat =  paste0("<p>Switch between long and wide formats of input data. ",
+                           "TCI accepts CSV or compressed CSV files (gz or bz2).</p>",
+                           "<p><b>Long format</b> - a row is a single data point and consecutive time series are arranged vertically. ",
+                           "Data file should contain at least 3 columns separated with a comma:</p>",
+                           "<li>Identifier of a time series</li>",
+                           "<li>Time points</li>",
+                           "<li>A time-varying variable</li>",
+                           "<br>",
+                           "<p><b>Wide format</b> - a row is a time series with columns as time points.",
+                           "At least 3 columns shuold be present:</p>",
+                           "<li>First two columns in wide format should contain grouping and track IDs</li>",
+                           "<li>A column with a time point. Headers of columns with time points need to be numeric</li>"), #2
   'Generate 60 random synthetic time series distributed evenly among 6 groups. Every time series has 60 time points.',             #3
   'Load CSV file with a column of track IDs for removal. IDs should correspond to those used for plotting.',                       #4
   'Load CSV file with 5 columns: grouping, start and end tpts of stimulation, start and end of y-position, dummy column with ID.', #5
@@ -193,7 +203,9 @@ helpText.server = c(
   'Calculate fold-change and z-score using the median and Median Absolute Deviation, instead of the mean and sd.',                 #14
   'Normalise to mean/median of selected time calculated globally, per group, or for individual time series.',                      #15
   'Download time series after modification in this section.',                                                                      #16
-  alertNAsPresent = "NAs present in the measurement column. Consider interpolation."
+  alertNAsPresent = "NAs present in the measurement column. Consider interpolation.",
+  alertWideMissesNumericTime = "Non-numeric headers of time columns. Data in wide format should have numeric column headers corresponding to time points.",
+  alertWideTooFewColumns = "Insufficient columns. Data in wide format should contain at least 3 columns: grouping, track ID, and a single time point."
 )
 
 # Functions for data processing ----

modules/tabClHier.R

@@ -22,6 +22,11 @@ clustHierUI <- function(id, label = "Hierarchical CLustering") {
   
   tagList(
     h4('Hierarchical clustering'),
+    p("Standard approach using R's ",
+      a("dist", href = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/dist.html"),
+      " and ",
+      a("hclust", href = "https://stat.ethz.ch/R-manual/R-devel/library/stats/html/hclust.html"),
+      " functions."),
     br(),
     fluidRow(
       column(4,

modules/tabClHierSpar.R

@@ -5,6 +5,17 @@
 # This module is for sparse hierarchical clustering using sparcl package
 #
 
+helpText.clHierSpar = c(alImportance = paste0("<p>Weight factors (WF) calculated during clustering ",
+                                              "reflect the importance of time points in the clustering. ",
+                                              "The following labels are used to indicate the importance:",
+                                              "<li>Black - time point not taken into account</li>",
+                                              "<li><p, style=\"color:DodgerBlue;\">* - low, WF∈(0, 0.1]</p></li>",
+                                              "<li><p, style=\"color:MediumSeaGreen;\">** - medium, WF∈(0.1, 0.5]</p></li>",
+                                              "<li><p, style=\"color:Tomato;\">*** - high, WF∈(0.5, 1.0]</p></li>",
+                                              "</p><p>Witten and Tibshirani (2010): ",
+                                              "<i>A framework for feature selection in clustering</i>; ",
+                                              "Journal of the American Statistical Association 105(490): 713-726.</p>"))
+
 # UI ----
 clustHierSparUI <- function(id, label = "Sparse Hierarchical CLustering") {
   ns <- NS(id)
@@ -14,6 +25,8 @@ clustHierSparUI <- function(id, label = "Sparse Hierarchical CLustering") {
       "Sparse hierarchical clustering using ",
       a("sparcl", href = "https://cran.r-project.org/web/packages/sparcl/")
     ),
+    p("Columns in the heatmap labeled according to their ",
+      actionLink(ns("alImportance"), "importance.")),
     br(),
     fluidRow(
       column(
@@ -158,9 +171,6 @@ clustHierSparUI <- function(id, label = "Sparse Hierarchical CLustering") {
                br(),
                downPlotUI(ns('downPlotHierSparHM'), "Download PNG"),
                actionButton(ns('butPlotHierSparHeatMap'), 'Plot!'),
-               br(),
-               "Columns in the heatmap labeled according to their ",
-               actionLink(ns("alImportance"), "importance"),
                withSpinner(plotOutput(ns('outPlotHierSpar')))
 
       ),
@@ -627,16 +637,7 @@ clustHierSpar <- function(input, output, session,
   addPopover(session, 
              ns("alImportance"),
              title = "Variable importance",
-             content = paste0("<p>Weight factors (WF) calculated during clustering ",
-                              "reflect the importance of time points in the clustering. ",
-                              "The following labels are used to indicate the importance:",
-                              "<li>Black - time point not taken into account</li>",
-                              "<li><p, style=\"color:DodgerBlue;\">* - low, WF∈(0, 0.1]</p></li>",
-                              "<li><p, style=\"color:MediumSeaGreen;\">** - medium, WF∈(0.1, 0.5]</p></li>",
-                              "<li><p, style=\"color:Tomato;\">*** - high, WF∈(0.5, 1.0]</p></li>",
-                              "</p><p>Witten and Tibshirani (2010): ",
-                              "<i>A framework for feature selection in clustering</i>; ",
-                              "Journal of the American Statistical Association 105(490): 713-726.</p>"),
+             content = helpText.clHierSpar[["alImportance"]],
              trigger = "click")
 
 }

ui.R

@@ -26,10 +26,9 @@ shinyUI(fluidPage(
         'Select data file and click "Load Data"',
         accept = c('text/csv', 'text/comma-separated-values,text/plain')
       ),
-      bsTooltip('inFileLoadNuc', helpText.server[1], placement = "top", trigger = "hover", options = NULL),
 
-      radioButtons("inRbutLongWide", "Data format:", c("Long" = 0, "Wide" = 1), inline = T),
-      bsTooltip('inRbutLongWide', helpText.server[2], placement = "top", trigger = "hover", options = NULL),
+      radioButtons("inRbutLongWide", actionLink("alDataFormat", "Data Format:"), c("Long" = 0, "Wide" = 1), inline = T),
+      bsAlert("alertAnchorSidePanelDataFormat"),
       
       actionButton("inButLoadNuc", "Load Data"),
       actionButton("butReset", "Reset file input"),