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update vignettes

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117445 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 13/05/2016 08:54:57
Showing 6 changed files

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@@ -1,5 +1,8 @@
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 CHANGES IN VERSION 1.5.3
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 ------------------------
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+ o add examples in vignettes <2016-05-13, Fri>
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+   + add fan layout example in treeVisualization vignette
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+   + add open_tree and rotate_tree example in treeManipulation vignette
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  o add angle in ggtree function, fan layout supported <2016-05-12, Thu>
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  o rotate_tree and open_tree function <2016-05-12, Thu> 
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  o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <2016-05-12, Thu>
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new file mode 100644
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Binary files /dev/null and b/vignettes/figures/fan_layout.gif differ
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new file mode 100644
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Binary files /dev/null and b/vignettes/figures/rotate_clade.gif differ
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new file mode 100644
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Binary files /dev/null and b/vignettes/figures/rotate_tree.gif differ
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@@ -222,6 +222,19 @@ p2 <- rotate(p, 21) %>% rotate(17)
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 multiplot(p, p2, ncol=2)
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 ```
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+```{r eval=F}
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+set.seed(2016-05-29)
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+p <- ggtree(tree <- rtree(50)) + geom_tiplab()
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+for (n in reorder(tree, 'postorder')$edge[,1] %>% unique) {
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+    p <- rotate(p, n)
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+    print(p + geom_point2(aes(subset = (node == n)), color='red'))
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+}
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+```
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+
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+![](figures/rotate_clade.gif)
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+
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+
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+
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 # flip clade
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 The positions of two selected clades (should share a same parent) can be flip over using __`flip`__ function.
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 ```{r fig.width=8, fig.height=4}
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 multiplot(p, flip(p, 17, 21), ncol=2)
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 ```
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+
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+
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+# open tree
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+
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+`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.
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+
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+```{r eval=FALSE}
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+set.seed(123)
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+tr = rtree(50)
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+
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+p <- ggtree(tr, layout='circular') + geom_tiplab2()
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+
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+for (angle in seq(0, 270, 10)) {
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+    print(open_tree(p, angle=angle) + ggtitle(paste("open angle:", angle)))
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+}
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+```
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+
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+![](figures/fan_layout.gif)
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+
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+
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+# rotate tree
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+
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+Rotating a `circular` tree is supported by `rotate_tree` function.
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+
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+```{r eval=FALSE}
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+for (angle in seq(0, 270, 10)) {
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+    print(rotate_tree(p, angle) + ggtitle(paste("rotate angle:", angle)))
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+}
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+```
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+
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+![](figures/rotate_tree.gif)
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@@ -74,7 +74,8 @@ Currently, _`ggtree`_ supports several layouts, including:
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 + `rectangular` (by default)
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 + `slanted`
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-+ `fan` or `circular`
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++ `circular`
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++ `fan`
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 for `Phylogram` (by default) and `Cladogram` if user explicitly setting `branch.length='none'`.
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 `ggtree` also supports `unrooted` layout.
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@@ -100,6 +101,13 @@ __`circular`__
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 ggtree(tree, layout="circular") + ggtitle("(Phylogram) circular layout")
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 ```	
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+__`fan`__
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+
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+```{r fig.height=5, fig.width=5, fig.align="center"}
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+ggtree(tree, layout="fan", open.angle=180) + ggtitle("(Phylogram) circular layout")
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+```	
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+
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+
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 ## Cladogram
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 __`rectangular`__
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 ggtree(tree, layout="circular", branch.length="none") + ggtitle("(Cladogram) circular layout")
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 ```
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+__`fan`__
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+
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+```{r fig.height=5, fig.width=5, fig.align="center"}
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+ggtree(tree, layout="fan", open.angle=180, branch.length="none") + ggtitle("(Cladogram) circular layout")
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+```	
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+
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+
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 ## Unrooted
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 Unrooted layout was implemented by the _`equal-angle algorithm`_ that described in _Inferring Phylogenies_[@felsenstein_inferring_2003 pp.578-580].