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

 Package: ggtree

 Type: Package

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

-Version: 1.1.5

+Version: 1.1.6

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -15,6 +15,7 @@ export("%<+%")

 export("%>%")

 export(.)

 export(add_colorbar)

+export(add_legend)

 export(aes)

 export(as.binary)

 export(collapse)

@@ -40,6 +41,7 @@ export(getNodeNum)

 export(getRoot)

 export(ggplotGrob)

 export(ggtree)

+export(gheatmap)

 export(gplot)

 export(groupClade)

 export(groupOTU)

@@ -59,6 +61,7 @@ export(read.tree)

 export(rtree)

 export(scaleClade)

 export(scale_color)

+export(scale_x_heatmap)

 export(theme_tree)

 export(theme_tree2)

 export(write.jplace)

@@ -1,3 +1,9 @@

+CHANGES IN VERSION 1.1.6

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

+ o add example of add_legend and gheatmap in vignette <2015-05-18, Mon> 

+ o gheatmap implementation of gplot <2015-05-18, Mon>

+ o add_legend for adding evolution distance legend <2015-05-18, Mon>

+ 

 CHANGES IN VERSION 1.1.5

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

  o implement scaleClade <2015-05-12, Tue>

@@ -488,3 +488,41 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {

                  ymax = ymax, fill=legend[,2], color=legend[,2]) 

 }

+

+##' add evolution distance legend

+##'

+##' 

+##' @title add_legend

+##' @param p tree view

+##' @param x x position

+##' @param y y position

+##' @param offset offset of text and line

+##' @param font.size font size

+##' @param ... additional parameter

+##' @return tree view

+##' @export

+##' @author Guangchuang Yu

+add_legend <- function(p, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {

+    if (is.null(x)) {

+        x <- min(p$data$x)

+    }

+    if (is.null(y)) {

+        y <- -0.5

+    }

+

+    d <- p$data$x %>% range %>% diff

+    d <- d/20 

+    n <- 0

+    while (d < 1) {

+        d <- d*10

+        n <- n + 1

+    }

+    d <- floor(d)/(10^n)

+    if (is.null(offset)) {

+        offset <- p$data$y %>% range %>% diff

+        offset <- offset / 100

+    }

+    p <- p + geom_segment(x=x, y=y, xend=x+d, yend=y, ...) +

+        geom_text(x=x+d/2, y=y+offset, label=d, size=font.size, ...)

+    return(p)

+}

@@ -1,3 +1,86 @@

+##' append a heatmap of a matrix to right side of phylogenetic tree

+##'

+##' 

+##' @title gheatmap

+##' @param p tree view

+##' @param data matrix or data.frame

+##' @param offset offset of heatmap to tree

+##' @param width width of each cell in heatmap

+##' @param low color of lowest value

+##' @param high color of highest value

+##' @param color color of heatmap cell border

+##' @param colnames logical, add matrix colnames or not

+##' @param font.size font size of matrix colnames

+##' @return tree view

+##' @importFrom reshape2 melt

+##' @importFrom ggplot2 geom_tile

+##' @importFrom ggplot2 geom_text

+##' @export

+##' @author Guangchuang Yu

+gheatmap <- function(p, data, offset=0, width=NULL, low="green", high="red",

+                     color="white", colnames=TRUE, font.size=4) {

+    if (is.null(width)) {

+        width <- (p$data$x %>% range %>% diff)/30

+    }

+    

+    isTip <- x <- y <- variable <- value <- from <- to <- NULL

+ 

+    df=p$data

+    df=df[df$isTip,]

+    start <- max(df$x) + offset

+

+    dd <- data[df$label[order(df$y)],]

+    dd$y <- sort(df$y)

+

+    dd$lab <- rownames(dd)

+    dd <- melt(dd, id=c("lab", "y"))

+    

+    if (any(dd$value == "")) {

+        dd$value[dd$value == ""] <- NA

+    }

+

+    V2 <- start + as.numeric(dd$variable) * width

+    mapping <- data.frame(from=dd$variable, to=V2)

+    mapping <- unique(mapping)

+

+    dd$x <- V2

+

+    p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), color=color)

+

+    if (is(dd$value,"numeric")) {

+        p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")

+    } else {

+        p2 <- p2 + scale_fill_discrete(na.value="white")

+    }

+    

+    if (colnames) {

+        p2 <- p2 + geom_text(data=mapping, aes(x=to, label=from), y=0, size=font.size)

+    }

+    

+    attr(p2, "mapping") <- mapping

+    return(p2)

+}

+

+##' scale x for tree with heatmap

+##'

+##' 

+##' @title scale_x_heatmap

+##' @param p tree view

+##' @param breaks breaks for tree

+##' @param labels lables for corresponding breaks

+##' @return tree view

+##' @importFrom ggplot2 scale_x_continuous

+##' @export

+##' @author Guangchuang Yu

+scale_x_heatmap <- function(p, breaks, labels=NULL) {

+    m <- attr(p, "mapping")

+    if (is.null(labels)) {

+        labels <- breaks

+    }

+    p + scale_x_continuous(breaks=c(breaks, m$to), labels=c(labels, as.character(m$from)))

+}

+

+

 ##' view tree and associated matrix

 ##'

 ##' @title gplot

@@ -6,6 +89,7 @@

 ##' @param low low color

 ##' @param high high color

 ##' @param widths widths of sub plot

+##' @param color color

 ##' @param font.size font size

 ##' @return list of figure

 ##' @importFrom gridExtra grid.arrange

@@ -21,12 +105,12 @@

 ##' rownames(d) <- tree$tip.label

 ##' colnames(d) <- paste0("G", 1:4)

 ##' gplot(p, d, low="green", high="red")

-gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), font.size=14) {

+gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), color="white", font.size=14) {

     ## p <- p + scale_x_continuous(expand = c(0, 0)) + scale_y_continuous(expand = c(0, 0.6))

     p1 <- p + scale_y_continuous(expand = c(0, 0.6))

     ## p1 <- p + theme(panel.margin=unit(0, "null"))

     ## p1 <- p1 + theme(plot.margin = unit(c(1, -1, 1.5, 1), "lines"))

-    p2 <- gplot.heatmap(p, data, low, high, font.size)

+    p2 <- gplot.heatmap(p, data, low, high, color, font.size)

     grid.arrange(p1, p2, ncol=2, widths=widths)

     invisible(list(p1=p1, p2=p2))

 }

@@ -41,7 +125,7 @@ gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), font.siz

 ##' @importFrom ggplot2 guides

 ##' @importFrom ggplot2 guide_legend

 ##' @importFrom reshape2 melt

-gplot.heatmap <- function(p, data, low, high, font.size) {

+gplot.heatmap <- function(p, data, low, high, color="white", font.size) {

     isTip <- x <- Var1 <- Var2 <- value <- NULL

     dd=melt(as.matrix(data))

     ## p <- ggtree(tree) ## + theme_tree2()

@@ -55,7 +139,7 @@ gplot.heatmap <- function(p, data, low, high, font.size) {

         dd$value[dd$value == ""] <- NA

     }

-    p2 <- ggplot(dd, aes(Var2, Var1, fill=value))+geom_tile(color="black")

+    p2 <- ggplot(dd, aes(Var2, Var1, fill=value))+geom_tile(color=color)

     if (is(dd$value,"numeric")) {

         p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")

     } else {

new file mode 100644

@@ -0,0 +1,31 @@

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/ggtree.R

+\name{add_legend}

+\alias{add_legend}

+\title{add_legend}

+\usage{

+add_legend(p, x = NULL, y = NULL, offset = NULL, font.size = 4, ...)

+}

+\arguments{

+\item{p}{tree view}

+

+\item{x}{x position}

+

+\item{y}{y position}

+

+\item{offset}{offset of text and line}

+

+\item{font.size}{font size}

+

+\item{...}{additional parameter}

+}

+\value{

+tree view

+}

+\description{

+add evolution distance legend

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,38 @@

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/gplot.R

+\name{gheatmap}

+\alias{gheatmap}

+\title{gheatmap}

+\usage{

+gheatmap(p, data, offset = 0, width, low = "green", high = "red",

+  color = "white", colnames = TRUE, font.size = 4)

+}

+\arguments{

+\item{p}{tree view}

+

+\item{data}{matrix or data.frame}

+

+\item{offset}{offset of heatmap to tree}

+

+\item{width}{width of each cell in heatmap}

+

+\item{low}{color of lowest value}

+

+\item{high}{color of highest value}

+

+\item{color}{color of heatmap cell border}

+

+\item{colnames}{logical, add matrix colnames or not}

+

+\item{font.size}{font size of matrix colnames}

+}

+\value{

+tree view

+}

+\description{

+append a heatmap of a matrix to right side of phylogenetic tree

+}

+\author{

+Guangchuang Yu

+}

+

@@ -5,7 +5,7 @@

 \title{gplot}

 \usage{

 gplot(p, data, low = "green", high = "red", widths = c(0.5, 0.5),

-  font.size = 14)

+  color = "white", font.size = 14)

 }

 \arguments{

 \item{p}{tree view}

@@ -18,6 +18,8 @@ gplot(p, data, low = "green", high = "red", widths = c(0.5, 0.5),

 \item{widths}{widths of sub plot}

+\item{color}{color}

+

 \item{font.size}{font size}

 }

 \value{

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/gplot.R

+\name{scale_x_heatmap}

+\alias{scale_x_heatmap}

+\title{scale_x_heatmap}

+\usage{

+scale_x_heatmap(p, breaks, labels = NULL)

+}

+\arguments{

+\item{p}{tree view}

+

+\item{breaks}{breaks for tree}

+

+\item{labels}{lables for corresponding breaks}

+}

+\value{

+tree view

+}

+\description{

+scale x for tree with heatmap

+}

+\author{

+Guangchuang Yu

+}

+

@@ -141,7 +141,15 @@ User can use _`ggtree(object)`_ command to view the phylogenetic tree directly,

 ## display evolution distance

-To show evolution distance, we can use `theme_tree2()` or `ggtree(showDistance=TRUE)`

+To show evolution distance, user can use `add_legend` function.

+

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

+ggtree(tree) %>% add_legend(x=0, y=10, offset=0.5, font.size=3)

+```

+

+User can specific the position and offset of distance from text to line segment.

+

+We can also use `theme_tree2()` or `ggtree(showDistance=TRUE)`

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

 ggtree(tree) + theme_tree2()

@@ -155,12 +163,6 @@ ggtree(tree, showDistance=TRUE) +

       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

@@ -748,6 +750,30 @@ p <- ggtree(beast_tree, time_scale=TRUE)+geom_tiplab(align=TRUE)+ xlim(1990, 201

 gplot(p, genotype, widths=c(5, 1))

 ```

+`gplot` function has [an issue](https://github.com/GuangchuangYu/ggtree/issues/3) that it can't always guarantee the heatmpa aligning to the tree properly, since the line up is between two figures and it's currently not supported internally by ggplot2. I have implemented another function `gheatmap` that can do the line up properly by creating a new layer above the tree.

+

+```{r fig.width=20, fig.height=16, fig.align="center"}

+p <- ggtree(beast_tree, time_scale=TRUE) %>% add_legend

+gheatmap(p, genotype, width=1)

+```

+

+The _width_ parameter is to control the width of each cell in the heatmap. It supports another parameter _offset_ for controling the distance between the tree and the heatmap, for instance left space for tip labels.

+

+```{r fig.width=20, fig.height=16, fig.align="center"}

+gheatmap(p+geom_tiplab(size=3), genotype, offset = 2, width=0.5)

+```

+

+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 over come this issue, we implemented `scale_x_heatmap` to set the x axis more reasonable. User can also use `gplot` and tweak the positions of two plot to align properly.

+

+```{r fig.width=20, fig.height=16, fig.align="center"}

+p <- ggtree(beast_tree, time_scale=TRUE) + geom_tiplab(size=3, align=TRUE) + theme_tree2()

+pp <- (p + scale_y_continuous(expand=c(0, 0.3))) %>%

+    gheatmap(genotype, offset=4, width=0.5, colnames=FALSE) %>%

+        scale_x_heatmap(breaks=seq(1992, 2013, by=5))

+pp + theme(legend.position="right")

+```

+

+

 # External documents