@@ -224,12 +224,14 @@ the [Tree Annotation](treeAnnotation.html) vignette.

 + [Tree Manipulation](treeManipulation.html)

 + [Tree Annotation](treeAnnotation.html)

 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)

-+ [Annotating phylogenetic tree with images](https://cran.r-project.org/web/packages/ggimage/vignettes/ggtree.html)

++ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-ggimage.html)

-More documents can be found in <https://guangchuangyu.github.io/ggtree>.

+**ggtree homepage**: <https://guangchuangyu.github.io/ggtree> (contains more

+information about the package, more documentation, a gallery of beautiful

+published images and links to related resources).

-# Feedback #

+# Feedback

  - For bugs or feature request, please post to [github issue](https://github.com/GuangchuangYu/ggtree/issues).

  - For user questions, please post to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree).

@@ -141,15 +141,16 @@ plot_grid(

 There are also other possible layouts that can be drawed by modifying

-scales/coordination, for examples, reverse label of time

-scale^[https://github.com/GuangchuangYu/ggtree/issues/87], repropotion

-circular/fan tree

-^[https://groups.google.com/d/msgid/bioc-ggtree/6db25ec7-ffb1-4776-bfe4-4a1ba239c8e8%40googlegroups.com], *etc.*.

+scales/coordination, for examples, [reverse label of time

+scale](https://github.com/GuangchuangYu/ggtree/issues/87), [repropotion

+circular/fan tree](

+https://groups.google.com/d/msgid/bioc-ggtree/6db25ec7-ffb1-4776-bfe4-4a1ba239c8e8%40googlegroups.com), *etc.*.

 ```{r eval=FALSE}

 ggtree(tr) + scale_x_reverse()

 ggtree(tr) + coord_flip()

 ggtree(tr) + scale_x_reverse() + coord_flip()

+print(ggtree(tr), newpage=TRUE, vp = grid::viewport(angle=-30, width=.9, height=.9))

 ggtree(tr, layout='slanted') + coord_flip()

 ggtree(tr, layout='slanted', branch.length='none') +

     coord_flip() + scale_y_reverse() +scale_x_reverse()

@@ -158,17 +159,22 @@ ggtree(tr) + scale_x_reverse() + coord_polar(theta='y')

 ggtree(tr) + scale_x_reverse(limits=c(10, 0)) + coord_polar(theta='y')

 ```

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

+```{r fig.keep='none', echo=FALSE, warning=FALSE}

+sv <- grid::grid.grabExpr(print(ggtree(tr), newpage=TRUE, vp = grid::viewport(angle=-30, width=.9, height=.9)))

+```

+

+```{r fig.width=8, fig.height = 8, echo=FALSE, warning=FALSE}

 plot_grid(

     ggtree(tr) + scale_x_reverse(),

     ggtree(tr) + coord_flip(),

     ggtree(tr) + scale_x_reverse() + coord_flip(),

+    sv,

     ggtree(tr, layout='slanted') + coord_flip(),

     ggtree(tr, layout='slanted', branch.length='none') + coord_flip() + scale_y_reverse() +scale_x_reverse(),

     ggtree(tr, layout='circular') + xlim(-10, NA),

     ggtree(tr) + scale_x_reverse() + coord_polar(theta='y'),

     ggtree(tr) + scale_x_reverse(limits=c(15, 0)) + coord_polar(theta='y'),

-    ncol = 4, labels = LETTERS[1:6])

+    ncol = 3, labels = LETTERS[1:9])

 ```

@@ -269,7 +275,7 @@ it also supports *image* geom to label tip with image files. A corresponding

 geom, `geom_nodelab` is also provided for displaying node labels. For details of

 label nodes with images, please refer to

 the vignette,

-[Annotating phylogenetic tree with images](https://cran.r-project.org/web/packages/ggimage/vignettes/ggtree.html).

+[Annotating phylogenetic tree with images](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-ggimage.html).