PSD: plot with color bar in clustering, inverse transform of axis, option to...

PSD: plot with color bar in clustering, inverse transform of axis, option to adjust period and frequency units

modules/auxfunc.R

@@ -229,6 +229,7 @@ LOCcalcPSD <- function(in.dt,
                     in.col.by,
                     in.method = "pgram",
                     in.return.period = TRUE,
+                    in.time.btwPoints = 1,
                     ...){
   require(data.table)
   # Method "ar" returns $spec as matrix whereas "pgram" returns a vector, custom function to homogenze output format
@@ -250,8 +251,11 @@ LOCcalcPSD <- function(in.dt,
   dt_agg <- dt_spec[, .(spec = mean(spec)), by = c(in.col.by, "freq")]
   if(in.return.period){
     dt_agg[, period := 1/freq]
-    dt_agg[, frequency := NULL]
+    dt_agg[, freq := NULL]
+    # Adjust period unit to go from frame unit  to time unit
+    dt_agg[, period := period * in.time.btwPoints]
   } else {
+    dt_agg[, freq := freq * (1/in.time.btwPoints)]
     setnames(dt_agg, "freq", "frequency")
   }
   return(dt_agg)
@@ -703,7 +707,7 @@ LOCplotPSD <- function(dt.arg, # input data table
                     group.arg=NULL, # string with column name for grouping time series (here, it's a column corresponding to grouping by condition)
                     xlab.arg = x.arg,
                     ylab.arg = y.arg,
-                    col.arg = NULL){
+                    facet.color.arg = NULL){
   require(ggplot2)
   if(length(setdiff(c(x.arg, y.arg, group.arg), colnames(dt.arg))) > 0){
     stop(paste("Missing columns in dt.arg: ", setdiff(c(x.arg, y.arg, group.arg), colnames(dt.arg))))
@@ -714,12 +718,18 @@ LOCplotPSD <- function(dt.arg, # input data table
     facet_wrap(group.arg) +
     labs(x = xlab.arg, y = ylab.arg)
   
-  if (is.null(col.arg)) {
-    p.tmp = p.tmp +
-      scale_color_discrete(name = '')
-  } else {
+  if (!is.null(facet.color.arg)) {
+    
+    loc.y.max = max(dt.arg[, c(y.arg), with = FALSE])
+    loc.dt.cl = data.table(xx = 1:length(facet.color.arg), yy = loc.y.max)
+    setnames(loc.dt.cl, 'xx', group.arg)
+    
+    # adjust facet.color.arg to plot
+    
     p.tmp = p.tmp +
-      scale_colour_manual(values = col.arg, name = '')
+      geom_hline(data = loc.dt.cl, colour = facet.color.arg, yintercept = loc.y.max, size = 4) +
+      scale_colour_manual(values = facet.color.arg,
+                          name = '')
   }
   
   return(p.tmp)

modules/trajPsdPlot.R

 require(DT)
+require(scales)
 
  # UI ----
 modPSDPlotUI =  function(id, label = "Plot PSD of average trajectory.") {
@@ -8,18 +9,19 @@ modPSDPlotUI =  function(id, label = "Plot PSD of average trajectory.") {
     fluidRow(
       column(
         3,
+        radioButtons(ns('rBPSDmethod'), 'Method for PSD estimation:', list('Smoothed Fourier' = 'pgram', 'AR Fit' = 'ar')),
         checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
         actionButton(ns('butPlotTraj'), 'Plot!')
       ),
       column(
         3,
-        selectInput(ns('inPSDxchoice'), 'Xaxis:', list('Period'= TRUE, 'Frequency'= FALSE)),
-        radioButtons(ns('rBPSDmethod'), 'Method for PSD estimation:', list('Smoothed Fourier' = 'pgram', 'AR Fit' = 'ar'))
+        selectInput(ns('inPSDxchoice'), 'X-axis:', list('Period'= TRUE, 'Frequency'= FALSE)),
+        numericInput(ns('ninPSDsamplFreq'), '# time units between 2 points:', value = 1, min = 0, step = 1)
       ),
       column(
         3,
-        selectInput(ns('inPSDlogtype'), 'Log function:', list('log2'= 'log2', 'log10'= 'log10', 'ln'= 'log')),
-        checkboxGroupInput(ns('chBGPSDlogaxis'), 'Log the axis:', list('x' = 'x', 'y' = 'y'), inline = TRUE)
+        selectInput(ns('inPSDlogtype'), 'Transformation:', list('1/x'='inverse_trans', 'log2'= 'log2', 'log10'= 'log10', 'ln'= 'log')),
+        checkboxGroupInput(ns('chBGPSDlogaxis'), 'Transform the axis:', list('x' = 'x', 'y' = 'y'), inline = TRUE)
       ),
       column(
         3,
@@ -43,9 +45,6 @@ modPSDPlotUI =  function(id, label = "Plot PSD of average trajectory.") {
       )
     ),
     uiOutput(ns('uiPlotTraj')),
-    br(),
-    modTrackStatsUI(ns('dispTrackStats')),
-    
     downPlotUI(ns('downPlotTraj'), "Download PDF")
   )
 }
@@ -187,7 +186,8 @@ modPSDPlot = function(input, output, session,
                               in.col.id = 'id',
                               in.col.by = in.facet,
                               in.method = input$rBPSDmethod,
-                              in.return.period = input$inPSDxchoice
+                              in.return.period = input$inPSDxchoice,
+                              in.time.btwPoints = input$ninPSDsamplFreq
                               )
     loc.dt.aggr[, (in.facet) := as.factor(get(in.facet))]
     
@@ -197,7 +197,7 @@ modPSDPlot = function(input, output, session,
                         x.arg = x_arg,
                         y.arg = 'spec',
                         group.arg = in.facet,
-                        col.arg = loc.facet.col,
+                        facet.color.arg = loc.facet.col,
                         xlab.arg = x_arg_str,
                         ylab.arg = '') +
       LOCggplotTheme(in.font.base = PLOTFONTBASE, 
@@ -205,11 +205,23 @@ modPSDPlot = function(input, output, session,
                      in.font.axis.title = PLOTFONTAXISTITLE, 
                      in.font.strip = PLOTFONTFACETSTRIP, 
                      in.font.legend = PLOTFONTLEGEND)
+    # TODO: Restore tick labels when using inverse transformation
+    # See: https://stackoverflow.com/questions/56130614/ggplot2-missing-labels-after-custom-scaling-of-axis
+    inverse_trans <- scales::trans_new("myinverse", transform = function(x) 1/x,
+                                       inverse = function(x) 1/(1/x))
     if("x" %in% input$chBGPSDlogaxis){
-      p.out <- p.out + scale_x_continuous(trans = input$inPSDlogtype)
+      if(input$inPSDlogtype == "inverse_trans"){
+        p.out <- p.out + scale_x_continuous(trans = inverse_trans)
+      } else {
+        p.out <- p.out + scale_x_continuous(trans = input$inPSDlogtype)
+      }
     }
     if("y" %in% input$chBGPSDlogaxis){
+      if(input$inPSDlogtype == "inverse_trans"){
+        p.out <- p.out + scale_y_continuous(trans = inverse_trans)
+      } else {
       p.out <- p.out + scale_y_continuous(trans = input$inPSDlogtype)
+      }
     }
     return(p.out)
   }