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

 CHANGES IN VERSION 1.3.9

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

+ o add 'multiPhylo' example in 'Tree Visualization' vignette <2016-01-13, Wed>

  o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.

    these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>

    + > ggtree(rtree(30)); viewClade(node=35) works. no need to pipe.

@@ -248,4 +248,31 @@ grid.arrange(

 	ncol=2)

 ```

+# Visualize a list of trees

+

+`ggtree` supports `multiPhylo` object and a list of trees can be view simultaneously.

+

+```{r fig.width=12, fig.height=4}

+trees <- lapply(c(10, 20, 40), rtree)

+class(trees) <- "multiPhylo"

+ggtree(trees) + facet_wrap(~.id, scale="free") + geom_tiplab()

+```

+

+One hundred bootstrap trees can also be view simultaneously.

+```{r fig.width=20, fig.height=20}

+btrees <- read.tree(system.file("extdata/RAxML", "RAxML_bootstrap.H3", package="ggtree"))

+ggtree(btrees) + facet_wrap(~.id, ncol=10)

+```

+

+Another way to view the bootstrap trees is to merge them together to form a density tree. We can add a layer of the best tree on the top of the density tree.

+

+```{r}

+p <- ggtree(btrees, layout="rectangular",   color="lightblue", alpha=.3)

+

+best_tree <- read.tree(system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree"))

+df <- fortify(best_tree, branch.length = 'none')

+p+geom_tree(data=df, color='firebrick')

+```

+

+

 # References