small update to graphical params

R/ggphylomorpho.R

@@ -10,6 +10,7 @@
 #' @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
+#' @param edge.width size parameter for edges drawn on phylomorphospace. Default is 1
 #' @return the ggplot object representing the phylomorphospace
 
 
@@ -22,7 +23,8 @@ ggphylomorpho <- function(tree,
                           title="Phylomorphospace",
                           xlab="PC1",
                           ylab="PC2",
-                          repel=TRUE)
+                          repel=TRUE,
+                          edge.width=1)
   {
 
   require(ggplot2)
@@ -62,13 +64,13 @@ ggphylomorpho <- function(tree,
 
   theplot <-
     ggplot() +
-    geom_segment(data=edgecoords,aes(x=x.x,xend=x.y, y=y.x, yend=y.y)) +
+    geom_segment(data=edgecoords,aes(x=x.x,xend=x.y, y=y.x, yend=y.y), size=edge.width) +
     geom_point(data=pointsForPlot, aes(x=x, y=y, color=color), size=5) +
     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))
+    theplot <- theplot + geom_text_repel(data=pointsForPlot, aes(x=x, y=y, label=label), segment.alpha=0.5)
   } else{
     theplot <- theplot + geom_text(data=pointsForPlot, aes(x=x, y=y, label=label))
   }

readme.md

@@ -28,13 +28,13 @@ head(sampleData$DF)
 ```
 
 ```
-##             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
+##              PC1       PC2 taxon  group
+## AAAAA -1.6961220 -3.166955 AAAAA group1
+## BBBBB -1.6417467 -3.020521 BBBBB group2
+## CCCCC -1.2058984 -3.519850 CCCCC group1
+## DDDDD -1.6926564 -1.302847 DDDDD group2
+## EEEEE  1.1066959 -1.219074 EEEEE group1
+## FFFFF  0.8772968 -1.233387 FFFFF group2
 ```
 
 ## check out the documentation for the function