@@ -6,7 +6,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

 csl: nature.csl

-output: 

+output:

   prettydoc::html_pretty:

     toc: true

     theme: cayman

@@ -99,13 +99,13 @@ __`circular`__

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

 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")

-```	

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

+```

 ## Cladogram

@@ -132,7 +132,7 @@ __`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

@@ -164,7 +164,7 @@ ggtree(tree2d, mrsd = "2014-05-01",

                theme(panel.grid.major.x=element_line(color="grey20", linetype="dotted", size=.3),

                      panel.grid.major.y=element_blank()) +

                          scale_y_continuous(labels=paste0("N", 2:7))

-```	

+```

 In this example, the figure demonstrates the quantity of __*y*__ increase along the trunk. User can highlight the trunk with different line size or color using the functions described in [Tree Manipulation](treeManipulation.html) vignette.

@@ -212,7 +212,7 @@ Showing all the internal nodes and tips in the tree can be done by adding a laye

 ```{r fig.width=3, fig.height=3, fig.align="center"}

 ggtree(tree)+geom_point(aes(shape=isTip, color=isTip), size=3)

 ```

- 

+

 ```{r fig.width=3, fig.height=3, fig.align="center"}

 p <- ggtree(tree) + geom_nodepoint(color="#b5e521", alpha=1/4, size=10)

 p + geom_tippoint(color="#FDAC4F", shape=8, size=3)