new file mode 100644

@@ -0,0 +1,30 @@

+add_range <- function(p, ...) {

+    df <- p$data

+    rr <- gsub("\\[", "", df$height_range)

+    rr <- gsub("\\]", "", rr)

+    rr2 <- strsplit(rr, split=',') %>% do.call('rbind', .)

+    rr2 <- matrix(as.numeric(rr2), ncol=2, byrow=FALSE)

+    ## if (!is.null(mrsd)) {

+    ##     mrsd %<>% as.Date

+    ##     date <- Date2decimal(mrsd)

+    ##     rr2 <- rr2 + date - max(rr2)

+    ##     if (asDate) {

+    ##         rr2 <- decimal2Date(rr2)

+    ##     }

+    ## }

+    rr2 <- rr2 + df$x - df$height

+    p + geom_segment2(x=rr2[,1], xend=rr2[,2], y=df$y, yend=df$y, ...)

+}

+

+## add range of height, only work with beast and only for height

+## when I have an idea of implementing such feature for all range

+## I will export it and make it usable for all users.

+##

+##

+## file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")

+## beast <- read.beast(file)

+## p <- ggtree(beast)

+## add_range(p, color='firebrick', size=2, alpha=.3)

+##

+## p <- ggtree(beast, mrsd='2013-01-01') + theme_tree2()

+## add_range(p, color='firebrick', size=2, alpha=.3)

@@ -111,11 +111,13 @@ get_clade_position <- function(treeview, node) {

 get_clade_position_ <- function(data, node) {

     sp <- get.offspring.df(data, node)

-    sp.df <- data[c(sp, node),]

+    ## sp.df <- data[c(sp, node),]

+    sp <- c(sp, node)

+    sp.df <- data[match(sp, data$node),]

     x <- sp.df$x

     y <- sp.df$y

     if ("branch.length" %in% colnames(data)) {

-        xmin <- min(x)-data[node, "branch.length"]/2

+        xmin <- min(x)-data[match(node, data$node), "branch.length"]/2

     } else {

         xmin <- min(sp.df$branch)

     }

@@ -93,8 +93,9 @@ phylopic <- function(tree_view, phylopic_id,

             if (is.null(node)) {

                 stop("node or x and y should not be NULL...")

             }

-            x <- tree_view$data[node, "x"]

-            y <- tree_view$data[node, "y"]

+            df <- tree_view$data

+            x <- df[match(node, df$node), "x"]

+            y <- df[match(node, df$node), "y"]

         }

         AR <- getAR(img)

         xmin <- x - width/2

@@ -53,7 +53,7 @@ p <- p + geom_tiplab(size=3)

 gheatmap(p, genotype, offset = 2, width=0.5)

 ```

-The _width_ parameter is to control the width of the heatmap. It supports another parameter _offset_ for controling the distance between the tree and the heatmap, for instance to allocate space for tip labels.

+The _width_ parameter is to control the width of the heatmap. It supports another parameter _offset_ for controlling the distance between the tree and the heatmap, for instance to allocate space for tip labels.

 For time-scaled tree, as in this example, it's more often to use x axis by using `theme_tree2`. But with this solution, the heatmap is just another layer and will change the `x` axis. To overcome this issue, we implemented `scale_x_ggtree` to set the x axis more reasonable. 

new file mode 100644

Binary files /dev/null and b/vignettes/figures/ggtree_objects_v2.png differ

@@ -35,7 +35,7 @@ library("ggtree")

 # Rescale tree

-Most of the phylogenetic trees are scaled by evolutionary distance (substitution/site), in `ggtree`, users can re-scale a phylogenetic tree by any numerical variable inferred by evolutionary analysis (e.g. *dN/dS*).

+Most of the phylogenetic trees are scaled by evolutionary distance (substitution/site). In `ggtree`, users can re-scale a phylogenetic tree by any numerical variable inferred by evolutionary analysis (e.g. *dN/dS*).

 ```{r fig.width=10, fig.height=5}

@@ -251,7 +251,7 @@ print(dd)

 knitr::kable(dd)

 ```

-We can imaging that the _`place`_ column stores the location we isolated the species and _`value`_ column stores numerical values (e.g. bootstrap values).

+We can imaging that the _`place`_ column stores the location that we isolated the species and _`value`_ column stores numerical values (e.g. bootstrap values).

 We have demonstrated using the operator, _`%<%`_, to update a tree view with a new tree. Here, we will introduce another operator, _`%<+%`_, that attaches annotation data to a tree view. The only requirement of the input data is that its first column should be matched with the node/tip labels of the tree.

@@ -89,14 +89,14 @@ Correspondingly, `ggtree` defines several `S4` classes to store evolutionary evi

 + _`raxml`_ for storing output of `read.raxml()`

-The _`jplace`_ class is also designed to store user specified annotation data, and serves as a standard format for tree annotation within the `ggtree` package. 

+The _`jplace`_ class is also designed to store user specified annotation data.

 Here is an overview of these `S4` classes:

-![](figures/ggtree_objects.png)

+![](figures/ggtree_objects_v2.png)

-In addition, `ggtree` also supports _`phylo`_, _`multiPhylo`_ (defined by `ape`[@paradis_ape_2004]) and _`phylo4`_ (defined by `phylobase`).

+In addition, `ggtree` also supports _`phylo`_, _`multiPhylo`_ (defined by `ape`[@paradis_ape_2004]), _`phylo4`_ (defined by `phylobase`) _`obkData`_ (defined in `OutbreakTools`) and _`phyloseq`_ (defined in `phyloseq`).

 In `ggtree`, tree objects can be merged and evidences inferred from different phylogenetic analyses can be combined or compared and visualized.

@@ -104,7 +104,7 @@ In `ggtree`, tree objects can be merged and evidences inferred from different ph

 Viewing a phylogenetic tree in `ggtree` is easy by using the command `ggtree(tree_object)` and annotating a phylogenetic tree is simple by adding graphic layers using the grammar of graphics.

-For each class, we defined _`get.fields`_ method to get the annotation features that available in the object that can be used to annotate a phylogenetic tree directly in `ggtree`. A _`get.tree`_ method can be used to convert tree object to `phylo` object that are widely supported by other `R` packages. 

+For each class, we defined _`get.fields`_ method to get the annotation features that available in the object that can be used to annotate a phylogenetic tree directly in `ggtree`. A _`get.tree`_ method can be used to convert tree object to `phylo` (or `multiPhylo` for `r8s`) object that are widely supported by other `R` packages. 

 The _`groupOTU`_ method is used for clustering related OTUs (from tips to their most recent common ancestor). Related OTUs are not necessarily within a clade, they can be distantly related. _`groupOTU`_ works fine for monophyletic (clade), polyphyletic and paraphyletic, while _`groupClade`_ only works for clade (monophyletic). These methods are useful for clustering related OTUs or clades.

@@ -308,7 +308,7 @@ msaplot(phylip, offset=1)

 ## Parsing EPA and pplacer output

-[EPA](http://sco.h-its.org/exelixis/web/software/epa/index.html)[@berger_EPA_2011] and [PPLACER](http://matsen.fhcrc.org/pplacer/)[@matsen_pplacer_2010] have common output file format, `jplace`, which can be parse by `read.jplace()` function. 

+[EPA](http://sco.h-its.org/exelixis/web/software/epa/index.html)[@berger_EPA_2011] and [PPLACER](http://matsen.fhcrc.org/pplacer/)[@matsen_pplacer_2010] have common output file format, `jplace`, which can be parsed by `read.jplace()` function. 

 ```{r}

 jpf <- system.file("extdata/sample.jplace",  package="ggtree")

@@ -37,7 +37,7 @@ flip <- ggtree::flip

 # Internal node number

-Some of the functions in `ggtree` works with clade and accepts a parameter of internal node number. To get the internal node number, user can use `geom_text2` to display it:

+Some of the functions in `ggtree` work with clade and accept a parameter of internal node number. To get the internal node number, user can use `geom_text2` to display it:

 ```{r}

 nwk <- system.file("extdata", "sample.nwk", package="ggtree")

@@ -45,7 +45,7 @@ tree <- read.tree(nwk)

 ggtree(tree) + geom_text2(aes(subset=!isTip, label=node), hjust=-.3) + geom_tiplab()

 ```

-Another way to get the internal node number is using `MRCA()` function by providing a vector of taxa names. The function will return node number of input taxa's most recent commond ancestor (MRCA). It works with tree object and graphic object.

+Another way to get the internal node number is using `MRCA()` function by providing a vector of taxa names. The function will return node number of input taxa's most recent commond ancestor (MRCA). It works with tree and graphic object.

 ```{r}

@@ -67,9 +67,9 @@ viewClade(p+geom_tiplab(), node=21)

 # group Clades

-The `ggtree` package defined several functions to manipulate tree view. _`groupClade`_ and _`groupOTU`_ methods for clustering clades or related OTUs. _`groupClade`_ accepts an internal node or a vector of internal nodes to cluster clade/clades.

+The `ggtree` package defined several functions to manipulate tree view. _`groupClade`_ and _`groupOTU`_ methods were designed for clustering clades or related OTUs. _`groupClade`_ accepts an internal node or a vector of internal nodes to cluster clade/clades.

-Both _`groupClade`_ and _`groupOTU`_ work fine with tree object or tree view.

+Both _`groupClade`_ and _`groupOTU`_ work fine with tree and graphic object.

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

 tree <- groupClade(tree, node=21)

@@ -32,7 +32,7 @@ library("ggtree")

 ```

-To view a phylogenetic tree, we first need to parse the tree file into `R`. The `ggtree` package supports many file format including output files of commonly used software packages in evolutionary biology. For more details, plase refer to the [Tree Data Import](treeImport.html) vignette.

+To view a phylogenetic tree, we first need to parse the tree file into `R`. The `ggtree` package supports many file formats including output files of commonly used software packages in evolutionary biology. For more details, plase refer to the [Tree Data Import](treeImport.html) vignette.

 ```{r}

 library("ggtree")

@@ -43,7 +43,7 @@ tree <- read.tree(nwk)

 # Viewing a phylogenetic tree with `ggtree`

 The `ggtree` package extends _`ggplot2`_ package to support viewing phylogenetic tree.

-It implements _`geom_tree`_ layer for displaying phylogenetic trees, as shown below:

+It implements _`geom_tree`_ layer for displaying phylogenetic tree, as shown below:

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

@@ -249,7 +249,7 @@ multiplot(

 # Visualize a list of trees

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

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

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

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