new file mode 100644

@@ -0,0 +1,4 @@

+.DS_Store

+R/.DS_Store

+vignettes/.DS_Store

+

@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 0.99.8

+Version: 0.99.9

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 0.99.9

+------------------------

+ o update vignette <2015-02-02, Mon>

+ 

 CHANGES IN VERSION 0.99.8

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

  o add get.phylopic function to read the online phylo pic and convert it to grob object,

@@ -28,6 +28,7 @@ BiocStyle::markdown()

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("ape")

+library("colorspace")

 library("ggplot2")

 library("ggtree")

 library("Biostrings")

@@ -135,7 +136,14 @@ ggtree(tree, showDistance=TRUE) +

       		vjust=-0.5, color="#F06C45") +

       scale_x_continuous(breaks=seq(0, 60, 5))

 ```

- 

+

+User can also use _`geom_segment`_ and _`geom_text`_ to specify the position and length of distance legend:

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

+ggtree(tree) +

+       geom_segment(x=0, y=12, xend=10, yend=12) +

+              geom_text(x=5, y=12.5, label=5, size=4)

+```

+

 ## display nodes/tips

 Show all the internal nodes and tips in the tree can be done by adding a layer of points using _`geom_point`_.

@@ -152,10 +160,19 @@ p + geom_point(color="#FDAC4F", shape=8, size=3, subset=.(isTip))

 ```

 ## display labels

+

+Users can use _`geom_text`_ to display the node/tip labels:

+

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

 p + geom_text(aes(label=label), size=3, color="purple", hjust=-0.3)

 ```

+For _`fan`_ and _`unrooted`_ layout, `r Githubpkg("GuangchuangYu/ggtree")` supports rotating node labels according to the angles of the branches.

+```{r fig.width=6, fig.height=6, warning=FALSE, fig.align="center"}

+ggtree(tree, layout="fan") + geom_text(aes(label=label, angle=angle), size=3, color="purple", vjust=-0.3)

+```

+

+

 By default, the positions are based on the node positions, we can change them to based on the middle of the branch/edge.

 ```{r fig.width=5, fig.height=3, warning=FALSE, fig.align="center"}

@@ -510,7 +527,7 @@ gplot(p2, dd, low="green", high="red", widths=c(.7, .3))

 ```{r fig.width=18, fig.height=10, fig.align="center"}

 library("ape")

 data(chiroptera)

-require(ggtree)

+library("ggtree")

 gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))

 ```

@@ -604,6 +621,18 @@ ggtree(tree_iris, color=cols[cls_ind]) %<+% species +

 This example demonstrates how the separation of the _`bionj`_ is very good with the _`setosa`_ species, but misses in labeling several _`versicolor`_ and _`virginica`_ species.

+## phylopic

+

+[PhyloPic](http://phylopic.org/) is a database that stores reusable silhouette images of organisms. `r Githubpkg("GuangchuangYu/ggtree")` supports downloading images from [PhyloPic](http://phylopic.org/) and annotating phylogenetic tree with the downloaded images.

+

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

+cols <- rainbow_hcl(2)

+x <- get.phylopic("d3563b54-780f-4711-a49a-7ea051e9dacc", size=512, color=cols[1], alpha=.3)

+y <- get.phylopic("3318565d-7531-4a8c-8b84-2e87dfae36ab", size=512, color=cols[2], alpha=.8)

+ggtree(tree) + annotation_custom(xmin=-Inf, ymin=-Inf, xmax=Inf, ymax=Inf, x) +

+       annotation_custom(xmin=15, ymin=2, xmax=25, ymax=4, y) 

+```

+

 # Session info