deleted file mode 100644

@@ -1,97 +0,0 @@

-title: "ggtree utilities"

-author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

-

-        School of Public Health, The University of Hong Kong"

-date: "`r Sys.Date()`"

-bibliography: ggtree.bib

-csl: nature.csl

-output:

-  prettydoc::html_pretty:

-    toc: true

-    theme: cayman

-    highlight: github

-  pdf_document:

-    toc: true

-vignette: >

-  %\VignetteIndexEntry{06 ggtree utilities}

-  %\VignetteEngine{knitr::rmarkdown}

-  %\usepackage[utf8]{inputenc}

-

-```{r style, echo=FALSE, results="asis", message=FALSE}

-knitr::opts_chunk$set(tidy = FALSE,

-		   message = FALSE)

-```

-

-

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

-library("ape")

-library("ggplot2")

-library("ggtree")

-```

-

-# Layers that allows subsetting

-

-`Subsetting` is not supported in layers defined in `ggplot2`, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s).

-

-In `ggtree`, we provides modified version of layers defined in `ggplot2` to support `subsetting`, including:

-

-+ geom_segment2

-+ geom_point2

-+ geom_text2

-+ geom_label2

-

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

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

-beast <- read.beast(file)

-ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), color='firebrick')

-```

-

-<!--

-

-# Multiple graphs on one page

-

-To support viewing multiple plots, ggtree provides `multiplot` function that similar to `gridExtra::grid.arrange` with extra feature of labeling the plots.

-

-

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

-multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))

-#```

-

-# subplots in ggplot object

-

-`ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object.

-

-#``` {r fig.width=8, fig.height=8, warning=F}

-set.seed(2016-01-04)

-tr <- rtree(30)

-tr <- groupClade(tr, node=45)

-p <- ggtree(tr, aes(color=group)) + geom_tippoint()

-p1 <- p + geom_hilight(node=45)

-p2 <- viewClade(p, node=45) + geom_tiplab()

-subview(p2, p1+theme_transparent(), x=2.3, y=28.5)

-#```

-

-This is the backend of the [inset](advanceTreeAnnotation.html) function.

-

-This `subview` function works with any `ggplot` objects and it had successful applied to [plot pie graphs on map](http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot/32380396#32380396).

-

-#``` {r eval=FALSE}

-library(ggtree)

-dd <- data.frame(x=LETTERS[1:3], y=1:3)

-pie <- ggplot(dd, aes(x=1, y, fill=x)) + geom_bar(stat="identity", width=1) + coord_polar(theta="y") + theme_inset()

-x <- sample(2:9)

-y <- sample(2:9)

-width <- sample(seq(0.05, 0.15, length.out=length(x)))

-height <- width

-p <- ggplot(data=data.frame(x=c(0, 10), y=c(0, 10)), aes(x, y))+geom_blank()

-for (i in seq_along(x)) {

-    p <- subview(p, pie, x[i], y[i], width[i], height[i])

-    print(p)

-}

-#```

-![](figures/subview_animation.gif)

-

-

@@ -48,16 +48,17 @@ beast <- read.beast(file)

 ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), color='firebrick')

 ```

+<!--

+

 # Multiple graphs on one page

 To support viewing multiple plots, ggtree provides `multiplot` function that similar to `gridExtra::grid.arrange` with extra feature of labeling the plots.

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

+#``` {r fig.width=8, fig.height=4, warning=FALSE}

 multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))

-```

+#```

-<!--

 # subplots in ggplot object

 `ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object.

@@ -53,15 +53,16 @@ ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), co

 To support viewing multiple plots, ggtree provides `multiplot` function that similar to `gridExtra::grid.arrange` with extra feature of labeling the plots.

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

+``` {r fig.width=8, fig.height=4, warning=FALSE}

 multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))

 ```

+<!--

 # subplots in ggplot object

 `ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object.

-```{r fig.width=8, fig.height=8, warning=F}

+#``` {r fig.width=8, fig.height=8, warning=F}

 set.seed(2016-01-04)

 tr <- rtree(30)

 tr <- groupClade(tr, node=45)

@@ -69,13 +70,13 @@ p <- ggtree(tr, aes(color=group)) + geom_tippoint()

 p1 <- p + geom_hilight(node=45)

 p2 <- viewClade(p, node=45) + geom_tiplab()

 subview(p2, p1+theme_transparent(), x=2.3, y=28.5)

-```

+#```

 This is the backend of the [inset](advanceTreeAnnotation.html) function.

 This `subview` function works with any `ggplot` objects and it had successful applied to [plot pie graphs on map](http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot/32380396#32380396).

-```{r eval=FALSE}

+#``` {r eval=FALSE}

 library(ggtree)

 dd <- data.frame(x=LETTERS[1:3], y=1:3)

 pie <- ggplot(dd, aes(x=1, y, fill=x)) + geom_bar(stat="identity", width=1) + coord_polar(theta="y") + theme_inset()

@@ -88,7 +89,8 @@ for (i in seq_along(x)) {

     p <- subview(p, pie, x[i], y[i], width[i], height[i])

     print(p)

 }

-```

+#```

 ![](figures/subview_animation.gif)

+-->

@@ -6,7 +6,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

 csl: nature.csl

-output: 

+output:

   prettydoc::html_pretty:

     toc: true

     theme: cayman

@@ -33,7 +33,7 @@ library("ggtree")

 # Layers that allows subsetting

-`Subsetting` is not supported in layers defined in `ggplot2`, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s). 

+`Subsetting` is not supported in layers defined in `ggplot2`, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s).

 In `ggtree`, we provides modified version of layers defined in `ggplot2` to support `subsetting`, including:

@@ -43,7 +43,7 @@ In `ggtree`, we provides modified version of layers defined in `ggplot2` to supp

 + geom_label2

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

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

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

 beast <- read.beast(file)

 ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), color='firebrick')

 ```

@@ -59,7 +59,7 @@ multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))

 # subplots in ggplot object

-`ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object. 

+`ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object.

 ```{r fig.width=8, fig.height=8, warning=F}

 set.seed(2016-01-04)

@@ -1,16 +1,16 @@

 ---

 title: "ggtree utilities"

-author: "\\

-

-	Guangchuang Yu (<guangchuangyu@gmail.com>) and Tommy Tsan-Yuk Lam (<ttylam@hku.hk>)\\

+author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

         School of Public Health, The University of Hong Kong"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

 csl: nature.csl

 output: 

-  html_document:

+  prettydoc::html_pretty:

     toc: true

+    theme: cayman

+    highlight: github

   pdf_document:

     toc: true

 vignette: >

@@ -57,7 +57,6 @@ To support viewing multiple plots, ggtree provides `multiplot` function that sim

 multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))

 ```

-

 # subplots in ggplot object

 `ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object. 

@@ -31,7 +31,6 @@ library("ggplot2")

 library("ggtree")

 ```

-

 # Layers that allows subsetting

 `Subsetting` is not supported in layers defined in `ggplot2`, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s). 

@@ -77,7 +77,7 @@ This is the backend of the [inset](advanceTreeAnnotation.html) function.

 This `subview` function works with any `ggplot` objects and it had successful applied to [plot pie graphs on map](http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot/32380396#32380396).

-```{r fig.show='animate', interval=.1}

+```{r eval=FALSE}

 library(ggtree)

 dd <- data.frame(x=LETTERS[1:3], y=1:3)

 pie <- ggplot(dd, aes(x=1, y, fill=x)) + geom_bar(stat="identity", width=1) + coord_polar(theta="y") + theme_inset()

@@ -91,5 +91,6 @@ for (i in seq_along(x)) {

     print(p)

 }

 ```

+![](figures/subview_animation.gif)

@@ -14,7 +14,7 @@ output:

   pdf_document:

     toc: true

 vignette: >

-  %\VignetteIndexEntry{00 ggtree introduction}

+  %\VignetteIndexEntry{06 ggtree utilities}

   %\VignetteEngine{knitr::rmarkdown}

   %\usepackage[utf8]{inputenc}

 ---

@@ -49,6 +49,16 @@ beast <- read.beast(file)

 ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), color='firebrick')

 ```

+# Multiple graphs on one page

+

+To support viewing multiple plots, ggtree provides `multiplot` function that similar to `gridExtra::grid.arrange` with extra feature of labeling the plots.

+

+

+```{r fig.width=8, fig.height=4, warning=FALSE}

+multiplot(ggtree(rtree(30)), ggtree(rtree(40)), ncol=2, labels=c('A', 'B'))

+```

+

+

 # subplots in ggplot object

 `ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object. 

new file mode 100644

@@ -0,0 +1,85 @@

+---

+title: "ggtree utilities"

+author: "\\

+

+	Guangchuang Yu (<guangchuangyu@gmail.com>) and Tommy Tsan-Yuk Lam (<ttylam@hku.hk>)\\

+

+        School of Public Health, The University of Hong Kong"

+date: "`r Sys.Date()`"

+bibliography: ggtree.bib

+csl: nature.csl

+output: 

+  html_document:

+    toc: true

+  pdf_document:

+    toc: true

+vignette: >

+  %\VignetteIndexEntry{00 ggtree introduction}

+  %\VignetteEngine{knitr::rmarkdown}

+  %\usepackage[utf8]{inputenc}

+---

+

+```{r style, echo=FALSE, results="asis", message=FALSE}

+knitr::opts_chunk$set(tidy = FALSE,

+		   message = FALSE)

+```

+

+

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

+library("ape")

+library("ggplot2")

+library("ggtree")

+```

+

+

+# Layers that allows subsetting

+

+`Subsetting` is not supported in layers defined in `ggplot2`, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s). 

+

+In `ggtree`, we provides modified version of layers defined in `ggplot2` to support `subsetting`, including:

+

++ geom_segment2

++ geom_point2

++ geom_text2

++ geom_label2

+

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

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

+beast <- read.beast(file)

+ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), color='firebrick')

+```

+

+# subplots in ggplot object

+

+`ggtree` implemented a function, `subview`, that can add subplots on a ggplot2 object. 

+

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

+set.seed(2016-01-04)

+tr <- rtree(30)

+tr <- groupClade(tr, node=45)

+p <- ggtree(tr, aes(color=group)) + geom_tippoint()

+p1 <- p + geom_hilight(node=45)

+p2 <- viewClade(p, node=45) + geom_tiplab()

+subview(p2, p1+theme_transparent(), x=2.3, y=28.5)

+```

+

+This is the backend of the [inset](advanceTreeAnnotation.html) function.

+

+This `subview` function works with any `ggplot` objects and it had successful applied to [plot pie graphs on map](http://stackoverflow.com/questions/10368180/plotting-pie-graphs-on-map-in-ggplot/32380396#32380396).

+

+```{r fig.show='animate', interval=.1}

+library(ggtree)

+dd <- data.frame(x=LETTERS[1:3], y=1:3)

+pie <- ggplot(dd, aes(x=1, y, fill=x)) + geom_bar(stat="identity", width=1) + coord_polar(theta="y") + theme_inset()

+x <- sample(2:9)

+y <- sample(2:9)

+width <- sample(seq(0.05, 0.15, length.out=length(x)))

+height <- width

+p <- ggplot(data=data.frame(x=c(0, 10), y=c(0, 10)), aes(x, y))+geom_blank()

+for (i in seq_along(x)) {

+    p <- subview(p, pie, x[i], y[i], width[i], height[i])

+    print(p)

+}

+```

+

+