Remove dependency on TCA package

modules/boxPlot.R

@@ -58,7 +58,7 @@ modBoxPlotUI =  function(id, label = "Plot Box-plots") {
         ),
         radioButtons(ns("rBAxisLabelsRotate"), "X-axis labels:",
                      c("horizontal" = 0,
-                       "45deg" = 45,
+                       "45 deg" = 45,
                        "90 deg" = 90))
       )
     ),
@@ -239,10 +239,9 @@ modBoxPlot = function(input, output, session,
       scale_fill_discrete(name = '') +
       xlab('') +
       ylab('') +
-      ggplotTheme() + 
-      #myGgplotTheme + 
+      LOCggplotTheme() + 
       theme(legend.position = input$selPlotBoxLegendPos,
-            axis.text.x = element_text(size = 12, angle = as.numeric(input$rBAxisLabelsRotate), hjust = ifelse(input$rBAxisLabelsRotate == 0, 0, 1)))
+            axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate)))
 
     
     return(p.out)

modules/clDistPlot.R

@@ -4,7 +4,7 @@ modClDistPlotUI =  function(id, label = "Plot Fractions WIthin Clusters") {
   tagList(
     radioButtons(ns("rBAxisLabelsRotate"), "X-axis labels:",
                  c("horizontal" = 0,
-                   "45deg" = 45,
+                   "45 deg" = 45,
                    "90 deg" = 90)),
     actionButton(ns('butPlotClDist'), 'Plot!'),
     plotOutput(ns('outPlotClDist'), height = '800px', width = 'auto'),
@@ -57,12 +57,11 @@ modClDistPlot = function(input, output, session, in.data, in.cols = NULL, in.fna
       scale_y_continuous(labels = percent) +
       ylab("percentage of cells\n") +  
       xlab("") +  
-      ggplotTheme() +
+      LOCggplotTheme() +
       theme(
-        axis.text.x = rotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate))
+        axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate))
     )
-      #myGgplotTheme
-    
+
     return(p.out)
     
   }

modules/tabClHier.R

@@ -430,7 +430,7 @@ clustHier <- function(input, output, session, in.data4clust, in.data4trajPlot, i
       loc.col.bounds = NULL
     
     
-    loc.p = myPlotHeatmap(loc.dm,
+    loc.p = LOCplotHeatmap(loc.dm,
                           loc.dend, 
                           palette.arg = input$selectPlotHierPalette, 
                           palette.rev.arg = input$inPlotHierRevPalette, 

modules/tabClHierSpar.R

@@ -488,7 +488,7 @@ clustHierSpar <- function(input, output, session, in.data4clust, in.data4trajPlo
       loc.col.bounds = NULL
     
     
-    loc.p = myPlotHeatmap(loc.dm,
+    loc.p = LOCplotHeatmap(loc.dm,
                           loc.dend, 
                           palette.arg = input$selectPlotHierSparPalette, 
                           palette.rev.arg = input$inPlotHierSparRevPalette, 

modules/tabScatter.R

@@ -196,7 +196,7 @@ plotScatter <- function() {
   
   #     loc.fit.rsq = ifelse(input$inRobustFit, loc.fit$r.squared, )
 
-  p.out = myGgplotScat(
+  p.out = LOCggplotScat(
     dt.arg = loc.dt,
     band.arg = NULL, #list(a = loc.fit$coeff.a, b = loc.fit$coeff.b, width = input$inBandWidth),
     group.col.arg = NULL,

modules/trajRibbonPlot.R

 require(DT)
-require(tca)
 
 modTrajRibbonPlotUI =  function(id, label = "Plot Individual Time Series") {
   ns <- NS(id)
@@ -194,7 +193,7 @@ modTrajRibbonPlot = function(input, output, session,
       loc.facet.col = loc.facet.col[loc.groups]
     }
     
-    loc.dt.aggr = tca::calcTrajCI(in.dt = loc.dt, 
+    loc.dt.aggr = LOCcalcTrajCI(in.dt = loc.dt, 
                              in.col.meas = 'y', 
                              in.col.by = c(in.facet, 'realtime'), 
                              in.type = 'normal')
@@ -211,8 +210,7 @@ modTrajRibbonPlot = function(input, output, session,
                            y.stim.arg = c('ystart', 'yend'),
                            xlab.arg = 'Time (min)',
                            ylab.arg = '') +
-      ggplotTheme() +
-      #myGgplotTheme +
+      LOCggplotTheme() +
       theme(legend.position = input$rBlegendPos)
     
     return(p.out)

server.R

@@ -15,12 +15,10 @@ library(d3heatmap) # for interactive heatmap
 library(dendextend) # for color_branches
 library(colorspace) # for palettes (used to colour dendrogram)
 library(RColorBrewer)
-# sparcl temporarily unavailable on CRAN
 library(sparcl) # sparse hierarchical and k-means
 library(scales) # for percentages on y scale
 library(dtw) # for dynamic time warping
 library(imputeTS) # for interpolating NAs
-library(tca) # for time series manipulatiom, e.g. normTraj, genTraj, plotTrajRibbon
 
 # change to increase the limit of the upload file size
 options(shiny.maxRequestSize = 200 * 1024 ^ 2)
@@ -46,7 +44,7 @@ shinyServer(function(input, output, session) {
   dataGen1 <- eventReactive(input$inDataGen1, {
     cat("dataGen1\n")
     
-    return(tca::genTraj(in.nwells = 3))
+    return(LOCgenTraj(in.nwells = 3))
   })
   
   # Load main data file
@@ -670,9 +668,9 @@ shinyServer(function(input, output, session) {
     }
     
     ## Normalization
-    # F-n tca::normTraj adds additional column with .norm suffix
+    # F-n normTraj adds additional column with .norm suffix
     if (input$chBnorm) {
-      loc.out = tca::normTraj(
+      loc.out = LOCnormTraj(
         in.dt = loc.out,
         in.meas.col = 'y',
         in.rt.col = 'realtime',