@@ -1,5 +1,6 @@

 CHANGES IN VERSION 1.5.2

 ------------------------

+ o add example of integrate user's data using phylo4d in treeAnnotation vignette <2016-05-11, Wed>

  o add extend, extendto parameter in geom_hilight <2016-05-10, Tue>

  o geom_hilight now supports hilight tips <2016-05-10, Tue>

    + https://github.com/GuangchuangYu/ggtree/issues/53

@@ -17,6 +17,7 @@ vignette: >

   %\VignetteIndexEntry{04 Tree Annotation}

   %\VignetteEngine{knitr::rmarkdown}

   %\VignetteDepends{phangorn}

+  %\VignetteDepends{phylobase}

   %\usepackage[utf8]{inputenc}

 ---

@@ -283,9 +284,23 @@ p+theme(legend.position="right")

 Once the data was attached, it is always attached. So that we can add other layers to display these information easily. 

 ```{r fig.width=6, fig.height=5, warning=FALSE, fig.align="center"}

 p + geom_text(aes(color=place, label=place), hjust=1, vjust=-0.4, size=3) +

-  geom_text(aes(color=place, label=value), hjust=1, vjust=1.4, size=3)

+    geom_text(aes(color=place, label=value), hjust=1, vjust=1.4, size=3)

 ```

+## phylo4d

+ 

+`phylo4d` was defined in the `phylobase` package, which can be employed to integrate user's data with phylogenetic tree. `phylo4d` was supported in `ggtree` and the data stored in the object can be used directly to annotate the tree.

+	  

+```{r fig.width=6, fig.height=5, warning=FALSE, fig.align="center"}

+dd2 <- dd[, -1]

+rownames(dd2) <- dd[,1]

+require(phylobase)

+tr2 <- phylo4d(tree, dd2)

+ggtree(tr2) + geom_tiplab(aes(color=place)) + 

+    geom_tippoint(aes(size=value, shape=place, color=place), alpha=0.25)

+```

+

+	

 ## jplace file format

 `ggtree` provides `write.jplace()` function to store user's own data and associated newick tree to a single `jplace` file, which can be parsed directly in `ggtree` and user's data can be used to annotate the tree directly. For more detail, please refer to the [Tree Data Import](treeImport.html#jplace-file-format) vignette.

@@ -96,7 +96,7 @@ Here is an overview of these `S4` classes:

 ![](figures/ggtree_objects_v2.png)

-In addition, `ggtree` also supports _`phylo`_, _`multiPhylo`_ (defined by `ape`[@paradis_ape_2004]), _`phylo4`_ (defined by `phylobase`) _`obkData`_ (defined in `OutbreakTools`) and _`phyloseq`_ (defined in `phyloseq`).

+In addition, `ggtree` also supports _`phylo`_, _`multiPhylo`_ (defined by `ape`[@paradis_ape_2004]), _`phylo4`_, _`phylo4d`_ (defined by `phylobase`) _`obkData`_ (defined in `OutbreakTools`) and _`phyloseq`_ (defined in `phyloseq`).

 In `ggtree`, tree objects can be merged and evidences inferred from different phylogenetic analyses can be combined or compared and visualized.