Comments and organisation

modules/auxfunc.R

@@ -6,11 +6,11 @@
 #
 
 
-require(ggplot2)
-require(RColorBrewer)
-require(gplots) # for heatmap.2
-require(grid) # for modifying grob
-require(Hmisc) # for CI calculation
+library(ggplot2)
+library(RColorBrewer)
+library(gplots) # for heatmap.2
+library(grid) # for modifying grob
+library(Hmisc) # for CI calculation
 
 
 # Global parameters ----

modules/dispStats.R

-require(DT)
-require(data.table)
+#
+# Time Course Inspector: Shiny app for plotting time series data
+# Author: Maciej Dobrzynski
+#
+# This module is for displaying stats in an interactive table using DT package
+#
 
+# UI ----
 modStatsUI =  function(id, label = "Comparing t-points") {
   ns <- NS(id)
   
@@ -11,7 +16,7 @@ modStatsUI =  function(id, label = "Comparing t-points") {
   )
 }
 
-
+# SERVER ----
 modStats = function(input, output, session, 
                    in.data, 
                    in.meascol = 'meas.y', 

modules/dispTrackStats.R

@@ -5,10 +5,6 @@
 # This module is for displaying time series statistics
 #
 
-require(DT)
-require(data.table)
-
-
 # UI ----
 modTrackStatsUI =  function(id, label = "Comparing t-points") {
   ns <- NS(id)

modules/tabAUC.R

@@ -6,8 +6,6 @@
 #
 # Calculates area under curve (AUC) for every single time course provided in the input
 
-require(pracma) # for trapz
-
 # UI ----
 modAUCplotUI =  function(id, label = "Plot Area Under Curves") {
   ns <- NS(id)

modules/tabScatter.R

@@ -14,11 +14,6 @@
 # callModule(clustHier, 'TabClustHier', dataMod)
 # where dataMod is the output from a reactive function that returns dataset ready for clustering
 
-
-require(plotly) # interactive plot
-require(robust)
-require(MASS)
-
 # UI ----
 tabScatterPlotUI <- function(id, label = "Comparing t-points") {
   ns <- NS(id)

modules/trajPlot.R

@@ -6,8 +6,6 @@
 #
 
 
-require(DT)
-
 # UI ----
 
 modTrajPlotUI =  function(id, label = "Plot Individual Time Series") {

modules/trajPsdPlot.R

@@ -5,9 +5,6 @@
 # This module is for plotting Power Spectral Analysis
 #
 
-require(DT)
-require(scales)
-
  # UI ----
 modPSDPlotUI =  function(id, label = "Plot PSD of average trajectory.") {
   ns <- NS(id)

modules/trajRibbonPlot.R

@@ -5,7 +5,6 @@
 # This module is for plotting group averages as ribbon plots (mean + 95%CI)
 #
 
-require(DT)
 
 modTrajRibbonPlotUI =  function(id, label = "Plot Individual Time Series") {
   ns <- NS(id)

server.R

@@ -10,15 +10,21 @@ library(shinyjs) #http://deanattali.com/shinyjs/
 library(data.table)
 library(ggplot2)
 library(gplots) # for heatmap.2
-library(plotly)
-#library(d3heatmap) # for interactive heatmap
+library(plotly) # interactive plot
+library(DT) # interactive tables
+
 library(dendextend) # for color_branches
 library(colorspace) # for palettes (used to colour dendrogram)
 library(RColorBrewer)
-library(sparcl) # sparse hierarchical and k-means
 library(scales) # for percentages on y scale
+
+library(sparcl) # sparse hierarchical and k-means
 library(dtw) # for dynamic time warping
 library(imputeTS) # for interpolating NAs
+library(robust) # for robust linear regression
+library(MASS)
+library(pracma) # for trapz
+
 
 # Global parameters ----
 # change to increase the limit of the upload file size