Defined global variables for font sizes in plots

modules/auxfunc.R

@@ -12,6 +12,18 @@ require(gplots) # for heatmap.2
 require(grid) # for modifying grob
 require(Hmisc) # for CI calculation
 
+
+# Global parameters ----
+# font sizes in pts for plots
+PLOTFONTBASE = 12
+PLOTFONTAXISTEXT = 12
+PLOTFONTAXISTITLE = 12
+PLOTFONTFACETSTRIP = 14
+PLOTFONTLEGEND = 12
+
+# default number of facets in plots
+PLOTNFACETDEFAULT = 3
+
 # Colour definitions ----
 rhg_cols <- c(
   "#771C19",
@@ -513,7 +525,11 @@ LOCplotTraj = function(dt.arg, # input data table
     xlab(paste0(xlab.arg, "\n")) +
     ylab(paste0("\n", ylab.arg)) +
     ggtitle(plotlab.arg) +
-    LOCggplotTheme() + 
+    LOCggplotTheme(in.font.base = PLOTFONTBASE, 
+                   in.font.axis.text = PLOTFONTAXISTEXT, 
+                   in.font.axis.title = PLOTFONTAXISTITLE, 
+                   in.font.strip = PLOTFONTFACETSTRIP, 
+                   in.font.legend = PLOTFONTLEGEND) + 
     theme(legend.position = "top")
   
   return(p.tmp)
@@ -655,7 +671,11 @@ LOCggplotScat = function(dt.arg,
   
   
   p.tmp = p.tmp +
-    LOCggplotTheme() +
+    LOCggplotTheme(in.font.base = PLOTFONTBASE, 
+                   in.font.axis.text = PLOTFONTAXISTEXT, 
+                   in.font.axis.title = PLOTFONTAXISTITLE, 
+                   in.font.strip = PLOTFONTFACETSTRIP, 
+                   in.font.legend = PLOTFONTLEGEND) + 
     theme(legend.position = "none")
 
   # Marginal distributions don;t work with plotly...

modules/boxPlot.R

@@ -239,7 +239,11 @@ modBoxPlot = function(input, output, session,
       scale_fill_discrete(name = '') +
       xlab('') +
       ylab('') +
-      LOCggplotTheme() + 
+      LOCggplotTheme(in.font.base = PLOTFONTBASE, 
+                     in.font.axis.text = PLOTFONTAXISTEXT, 
+                     in.font.axis.title = PLOTFONTAXISTITLE, 
+                     in.font.strip = PLOTFONTFACETSTRIP, 
+                     in.font.legend = PLOTFONTLEGEND) + 
       theme(legend.position = input$selPlotBoxLegendPos,
             axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate)))
 

modules/clDistPlot.R

@@ -57,7 +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("") +  
-      LOCggplotTheme() +
+      LOCggplotTheme(in.font.base = PLOTFONTBASE, 
+                     in.font.axis.text = PLOTFONTAXISTEXT, 
+                     in.font.axis.title = PLOTFONTAXISTITLE, 
+                     in.font.strip = PLOTFONTFACETSTRIP, 
+                     in.font.legend = PLOTFONTLEGEND) + 
       theme(
         axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate))
     )

modules/tabScatter.R

@@ -48,7 +48,7 @@ tabScatterPlotUI <- function(id, label = "Comparing t-points") {
         numericInput(
           ns('inPlotNcolFacet'),
           '#columns',
-          value = 2,
+          value = PLOTNFACETDEFAULT,
           min = 1,
           step = 1
         )

modules/trajPlot.R

@@ -20,7 +20,7 @@ modTrajPlotUI =  function(id, label = "Plot Individual Time Series") {
         numericInput(
           ns('inPlotTrajFacetNcol'),
           '#Columns:',
-          value = 4,
+          value = PLOTNFACETDEFAULT,
           min = 1,
           width = '100px',
           step = 1

modules/trajRibbonPlot.R

@@ -210,7 +210,11 @@ modTrajRibbonPlot = function(input, output, session,
                            y.stim.arg = c('ystart', 'yend'),
                            xlab.arg = 'Time (min)',
                            ylab.arg = '') +
-      LOCggplotTheme() +
+      LOCggplotTheme(in.font.base = PLOTFONTBASE, 
+                     in.font.axis.text = PLOTFONTAXISTEXT, 
+                     in.font.axis.title = PLOTFONTAXISTITLE, 
+                     in.font.strip = PLOTFONTFACETSTRIP, 
+                     in.font.legend = PLOTFONTLEGEND) + 
       theme(legend.position = input$rBlegendPos)
     
     return(p.out)

server.R

@@ -20,6 +20,7 @@ library(scales) # for percentages on y scale
 library(dtw) # for dynamic time warping
 library(imputeTS) # for interpolating NAs
 
+# Global parameters ----
 # change to increase the limit of the upload file size
 options(shiny.maxRequestSize = 200 * 1024 ^ 2)