diff scripts_R/MetadataPlots.R @ 91:d3e05cd49feb branch-tests

trying to plot wrt PLOSONE guidelines

--- a/scripts_R/MetadataPlots.R	Mon Oct 02 12:37:55 2017 +0100
+++ b/scripts_R/MetadataPlots.R	Mon Oct 02 15:32:51 2017 +0100
@@ -1,6 +1,13 @@
 library(rworldmap)
 library(ggplot2)
 
+library(extrafont)
+font_import()
+loadfonts()
+Arial <- Type1Font(family="Arial", metrics=c("ArialMT.afm","arial-BoldMT.afm","Arial-ItalicMT.afm", "Arial-BoldItalicMT.afm"))
+postscriptFonts(Arial=Arial)
+par(family="Arial")
+
 PlotBarChart<- function(df, cat="Language", ordercat="REGION", mincount=10, legend=T, color_plt="Paired"){
   idx_cat = which(colnames(df)==cat)
   idx_ordercat = which(colnames(df)==ordercat)
@@ -13,7 +20,7 @@
   #g = g+ylim("0", "100")#+scale_y_discrete(breaks=c("100"),labels=c("100+"))
   g=g+scale_y_continuous(limits=c(0, 200), breaks=seq(0,200,40))
   g=g+scale_fill_brewer(palette=color_plt)
-  g=g+theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5))
+  g=g+theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5), text = element_text(size=12))
   g=g+labs(y="Counts",x=cat)+coord_flip()+theme_bw()
   if (legend){
     g=g+guides(fill = guide_legend(title = ordercat))}
@@ -76,7 +83,11 @@
   #do.call( addMapLegend, c(mapParams, labelFontSize=0.7, legendWidth=0.5, tcl=0.3, legendMar = 7, legendLabels="all",horizontal=T, legendIntervals="page"))
   legend("left", legend = c(paste(seq(90,0,-10),'-',seq(100,10,-10),'%'), 'NA'), fill = c(heat.colors(10, alpha = 1), 'grey'), cex = 0.56, bty = "o",bg="white",box.lwd=0,box.col="white")
   if (output!=''){
-    pdf(output)
+    if (grepl('.pdf', output)){
+      pdf(output, pointsize=12)
+    } else if (grepl('.eps', output)){
+      postscript(output, pointsize=12)
+    }
     #mapParams <- mapCountryData(spdf, nameColumnToPlot="Outliers",catMethod=seq(0,70,5),missingCountryCol='grey',colourPalette='heat', mapTitle="", addLegend=FALSE)
     mapParams <- mapCountryData(spdf, nameColumnToPlot="Outliers", catMethod=seq(0,1,0.1), missingCountryCol='grey',colourPalette='heat', mapTitle="", addLegend=FALSE)
     #mapParams <- mapCountryData(spdf, nameColumnToPlot="Outliers", ylim=c(-60,90), catMethod=seq(0,1,0.1), missingCountryCol='grey',colourPalette='heat', mapTitle="", addLegend=FALSE)