add ggrepel functionality for labels

R/ggphylomorpho.R

@@ -9,6 +9,7 @@
 #' @param title the text string to use as the title of the phylomorphospace plot
 #' @param xlab the text label for the x axis
 #' @param ylab the text label for the y axis
+#' @param repel boolean indicating whether or not to use the \code{ggrepel} package to prevent overplotting of labels
 #' @return the ggplot object representing the phylomorphospace
 
 
@@ -20,11 +21,13 @@ ggphylomorpho <- function(tree,
                           labelvar=taxon,
                           title="Phylomorphospace",
                           xlab="PC1",
-                          ylab="PC2")
+                          ylab="PC2",
+                          repel=TRUE)
   {
 
   require(ggplot2)
   require(phytools)
+  require(ggrepel)
 
   ## create matrix for use in phytools::fastAnc()
   mat <- cbind(eval(substitute(xvar), tipinfo),eval(substitute(yvar), tipinfo))
@@ -61,9 +64,13 @@ ggphylomorpho <- function(tree,
     ggplot() +
     geom_segment(data=edgecoords,aes(x=x.x,xend=x.y, y=y.x, yend=y.y)) +
     geom_point(data=pointsForPlot, aes(x=x, y=y, color=color), size=5) +
-    geom_text(data=pointsForPlot, aes(x=x, y=y, label=label)) +
     labs(title=title, x=xlab, y=ylab) +
     theme_bw(20) +
     theme(legend.position='bottom')
+  if(repel){
+    theplot <- theplot + geom_text_repel(data=pointsForPlot, aes(x=x, y=y, label=label))
+  } else{
+    theplot <- theplot + geom_text(data=pointsForPlot, aes(x=x, y=y, label=label))
+  }
   return(theplot)
 }

R/makesampledata.R

@@ -1,10 +1,11 @@
 makesampledata <- function(){
   require(phytools)
-  tree<-pbtree(n=26,tip.label=LETTERS)
+  labs <- sapply(LETTERS, FUN=function(x) paste(rep(x, 5), collapse=""))
+  tree<-pbtree(n=26,tip.label=labs)
   DF <- data.frame(
     PC1=fastBM(tree),
     PC2=fastBM(tree),
-    taxon=LETTERS,
+    taxon=labs,
     group=rep(c("group1","group2"),13)
   )
   return(list(tree=tree, DF=DF))

readme.md

@@ -28,13 +28,13 @@ head(sampleData$DF)
 ```
 
 ```
-##           PC1         PC2 taxon  group
-## A -2.97831839  2.67580286     A group1
-## B -0.18117859 -1.14645602     B group2
-## C -0.69258460 -2.32020109     C group1
-## D -0.40664199  0.09467764     D group2
-## E -0.01512143  1.23078740     E group1
-## F  0.93301701  0.65321188     F group2
+##             PC1        PC2 taxon  group
+## AAAAA  1.416156 -3.4994342 AAAAA group1
+## BBBBB  2.364885 -3.1435084 BBBBB group2
+## CCCCC  3.923850 -3.7085053 CCCCC group1
+## DDDDD  4.779961 -3.1848266 DDDDD group2
+## EEEEE  1.433133  2.9528747 EEEEE group1
+## FFFFF -0.273229 -0.6153418 FFFFF group2
 ```
 
 ## check out the documentation for the function