@@ -1,5 +1,8 @@

 CHANGES IN VERSION 1.5.3

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

+ o add examples in vignettes <2016-05-13, Fri>

+   + add fan layout example in treeVisualization vignette

+   + add open_tree and rotate_tree example in treeManipulation vignette

  o add angle in ggtree function, fan layout supported <2016-05-12, Thu>

  o rotate_tree and open_tree function <2016-05-12, Thu> 

  o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <2016-05-12, Thu>

new file mode 100644

Binary files /dev/null and b/vignettes/figures/fan_layout.gif differ

new file mode 100644

Binary files /dev/null and b/vignettes/figures/rotate_clade.gif differ

new file mode 100644

Binary files /dev/null and b/vignettes/figures/rotate_tree.gif differ

@@ -222,6 +222,19 @@ p2 <- rotate(p, 21) %>% rotate(17)

 multiplot(p, p2, ncol=2)

 ```

+```{r eval=F}

+set.seed(2016-05-29)

+p <- ggtree(tree <- rtree(50)) + geom_tiplab()

+for (n in reorder(tree, 'postorder')$edge[,1] %>% unique) {

+    p <- rotate(p, n)

+    print(p + geom_point2(aes(subset = (node == n)), color='red'))

+}

+```

+

+![](figures/rotate_clade.gif)

+

+

+

 # flip clade

 The positions of two selected clades (should share a same parent) can be flip over using __`flip`__ function.

@@ -229,3 +242,34 @@ The positions of two selected clades (should share a same parent) can be flip ov

 ```{r fig.width=8, fig.height=4}

 multiplot(p, flip(p, 17, 21), ncol=2)

 ```

+

+

+# open tree

+

+`ggtree` supports `fan` layout and can also transform the `circular` layout tree to a `fan` tree by specifying an open `angle` to `open_tree` function.

+

+```{r eval=FALSE}

+set.seed(123)

+tr = rtree(50)

+

+p <- ggtree(tr, layout='circular') + geom_tiplab2()

+

+for (angle in seq(0, 270, 10)) {

+    print(open_tree(p, angle=angle) + ggtitle(paste("open angle:", angle)))

+}

+```

+

+![](figures/fan_layout.gif)

+

+

+# rotate tree

+

+Rotating a `circular` tree is supported by `rotate_tree` function.

+

+```{r eval=FALSE}

+for (angle in seq(0, 270, 10)) {

+    print(rotate_tree(p, angle) + ggtitle(paste("rotate angle:", angle)))

+}

+```

+

+![](figures/rotate_tree.gif)

@@ -74,7 +74,8 @@ Currently, _`ggtree`_ supports several layouts, including:

 + `rectangular` (by default)

 + `slanted`

-+ `fan` or `circular`

++ `circular`

++ `fan`

 for `Phylogram` (by default) and `Cladogram` if user explicitly setting `branch.length='none'`.

 `ggtree` also supports `unrooted` layout.

@@ -100,6 +101,13 @@ __`circular`__

 ggtree(tree, layout="circular") + ggtitle("(Phylogram) circular layout")

 ```	

+__`fan`__

+

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

+ggtree(tree, layout="fan", open.angle=180) + ggtitle("(Phylogram) circular layout")

+```	

+

+

 ## Cladogram

 __`rectangular`__

@@ -120,6 +128,13 @@ __`circular`__

 ggtree(tree, layout="circular", branch.length="none") + ggtitle("(Cladogram) circular layout")

 ```

+__`fan`__

+

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

+ggtree(tree, layout="fan", open.angle=180, branch.length="none") + ggtitle("(Cladogram) circular layout")

+```	

+

+

 ## Unrooted

 Unrooted layout was implemented by the _`equal-angle algorithm`_ that described in _Inferring Phylogenies_[@felsenstein_inferring_2003 pp.578-580].