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

 Package: ggtree

 Type: Package

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

-Version: 1.1.16

+Version: 1.1.17

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -71,6 +71,8 @@ export(rtree)

 export(scaleClade)

 export(scale_color)

 export(scale_x_ggtree)

+export(subview)

+export(theme_transparent)

 export(theme_tree)

 export(theme_tree2)

 export(write.jplace)

@@ -129,6 +131,7 @@ importFrom(ggplot2,geom_segment)

 importFrom(ggplot2,geom_text)

 importFrom(ggplot2,geom_tile)

 importFrom(ggplot2,ggplot)

+importFrom(ggplot2,ggplotGrob)

 importFrom(ggplot2,guide_legend)

 importFrom(ggplot2,guides)

 importFrom(ggplot2,labs)

@@ -1,3 +1,10 @@

+CHANGES IN VERSION 1.1.17

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

+ o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>

+ o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu> 

+ o theme_transparent to make background transparent <2015-08-27, Thu>

+ o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>  

+ 

 CHANGES IN VERSION 1.1.16

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

  o update citation <2015-08-17, Mon>

@@ -36,7 +36,12 @@ ggplotGrob <- ggplot2::ggplotGrob

 ##' @param stat The statistical transformation to use on the data for this layer

 ##' @param position The position adjustment to use for overlapping points on this layer

 ##' @param parse if TRUE, the labels will be passd into expressions

+##' @param show.legend logical

+##' @param inherit.aes logical

 ##' @param ... other arguments passed on to 'layer'

+##' @param nudge_x horizontal adjustment

+##' @param nudge_y vertical adjustment

+##' @param check_overlap if TRUE, text that overlaps previous text in the same layer will not be plotted

 ##' @source

 ##' This is just the imported function

 ##' from the ggplot2 package. The documentation you should

@@ -267,7 +267,7 @@ geom_tippoint <- function(...) {

 theme_tree <- function(bgcolor="white", fgcolor="black", ...) {

     theme_tree2() %+replace%

     theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),

-          axis.line.x = element_line(color=bgcolor),

+          axis.line.x = element_blank(),

           axis.text.x = element_blank(),

           axis.ticks.x = element_blank(),

           ...)

@@ -301,12 +301,32 @@ theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {

           panel.background=element_rect(fill=bgcolor, colour=bgcolor),

           panel.border=element_blank(),

           axis.line=element_line(color=fgcolor),

-          axis.line.y=element_line(color=bgcolor),

+          axis.line.y=element_blank(),

           axis.ticks.y=element_blank(),

           axis.text.y=element_blank(),

           ...)

 }

+##' transparent background theme

+##'

+##' 

+##' @title theme_transparent

+##' @param ... additional parameter to tweak the theme

+##' @return ggplot object

+##' @importFrom ggplot2 theme

+##' @importFrom ggplot2 element_rect

+##' @export

+##' @author Guangchuang Yu

+theme_transparent <- function(...) {

+    theme(panel.background = element_rect(

+              fill = "transparent",

+              colour = NA),

+          plot.background = element_rect(

+              fill = "transparent",

+              colour = NA), ...)

+}

+

+

 ##' hilight clade with rectangle

 ##'

 ##' 

@@ -642,6 +662,7 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {

 ##' 

 ##' @title add_legend

 ##' @param p tree view

+##' @param width width of legend

 ##' @param x x position

 ##' @param y y position

 ##' @param offset offset of text and line

@@ -654,7 +675,7 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {

 ##' @importFrom ggplot2 ylim

 ##' @export

 ##' @author Guangchuang Yu

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

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

     dx <- p$data$x %>% range %>% diff

     if (is.null(x)) {

@@ -666,14 +687,18 @@ add_legend <- function(p, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {

         p <- p + ylim(0, max(p$data$y))

     }

-

-    d <- dx/10 

-    n <- 0

-    while (d < 1) {

-        d <- d*10

-        n <- n + 1

+    if (is.null(width) || is.na(width)) {

+        d <- dx/10 

+        n <- 0

+        while (d < 1) {

+            d <- d*10

+            n <- n + 1

+        }

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

+    } else {

+        d <- width

     }

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

+    

     if (is.null(offset)) {

         offset <- 0.4

     }

@@ -10,6 +10,7 @@

 ##' @param high color of highest value

 ##' @param color color of heatmap cell border

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

+##' @param colnames_position one of 'bottom' or 'top'

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

 ##' @return tree view

 ##' @importFrom reshape2 melt

@@ -22,7 +23,10 @@

 ##' @export

 ##' @author Guangchuang Yu

 gheatmap <- function(p, data, offset=0, width=1, low="green", high="red",

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

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

+

+    colnames_position %<>% match.arg(c("bottom", "top"))

+    

     ## if (is.null(width)) {

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

     ## }

@@ -61,7 +65,12 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red",

     }

     if (colnames) {

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

+        if (colnames_position == "bottom") {

+            y <- 0

+        } else {

+            y <- max(p$data$y) + 1

+        }

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

     }

     p2 <- p2 + theme(legend.position="right", legend.title=element_blank())

new file mode 100644

@@ -0,0 +1,26 @@

+##' add subview to mainview for ggplot2 objects

+##'

+##' 

+##' @title subview

+##' @param mainview main view

+##' @param subview sub view

+##' @param x x position

+##' @param y y position

+##' @param width width of subview, [0,1]

+##' @param height height of subview, [0,1]

+##' @return ggplot object

+##' @importFrom ggplot2 annotation_custom

+##' @importFrom ggplot2 ggplotGrob

+##' @export

+##' @author Guangchuang Yu

+subview <- function(mainview, subview, x, y, width=.1, height=.1) {

+    xrng <- mainview$data$x %>% range %>% diff

+    yrng <- mainview$data$y %>% range %>% diff

+   

+    mainview + annotation_custom(

+        ggplotGrob(subview),

+        xmin = x - width*xrng,

+        xmax = x + width*xrng,

+        ymin = y - height*yrng,

+        ymax = y + height*yrng)

+}

@@ -4,11 +4,14 @@

 \alias{add_legend}

 \title{add_legend}

 \usage{

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

+add_legend(p, width = NULL, x = NULL, y = NULL, offset = NULL,

+  font.size = 4, ...)

 }

 \arguments{

 \item{p}{tree view}

+\item{width}{width of legend}

+

 \item{x}{x position}

 \item{y}{y position}

@@ -10,7 +10,9 @@ read for the geom_text function can be found here: \link[ggplot2]{geom_text}

 }

 \usage{

 geom_text(mapping = NULL, data = NULL, stat = "identity",

-  position = "identity", parse = FALSE, ...)

+  position = "identity", parse = FALSE, show.legend = NA,

+  inherit.aes = TRUE, ..., nudge_x = 0, nudge_y = 0,

+  check_overlap = FALSE)

 }

 \arguments{

 \item{mapping}{the aesthetic mapping}

@@ -24,7 +26,17 @@ only needed if you want to override he plot defaults.}

 \item{parse}{if TRUE, the labels will be passd into expressions}

+\item{show.legend}{logical}

+

+\item{inherit.aes}{logical}

+

 \item{...}{other arguments passed on to 'layer'}

+

+\item{nudge_x}{horizontal adjustment}

+

+\item{nudge_y}{vertical adjustment}

+

+\item{check_overlap}{if TRUE, text that overlaps previous text in the same layer will not be plotted}

 }

 \description{

 text annotations

@@ -5,7 +5,8 @@

 \title{gheatmap}

 \usage{

 gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",

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

+  color = "white", colnames = TRUE, colnames_position = "bottom",

+  font.size = 4)

 }

 \arguments{

 \item{p}{tree view}

@@ -24,6 +25,8 @@ gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",

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

+\item{colnames_position}{one of 'bottom' or 'top'}

+

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

 }

 \value{

new file mode 100644

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

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

+% Please edit documentation in R/subview.R

+\name{subview}

+\alias{subview}

+\title{subview}

+\usage{

+subview(mainview, subview, x, y, width = 0.1, height = 0.1)

+}

+\arguments{

+\item{mainview}{main view}

+

+\item{subview}{sub view}

+

+\item{x}{x position}

+

+\item{y}{y position}

+

+\item{width}{width of subview, [0,1]}

+

+\item{height}{height of subview, [0,1]}

+}

+\value{

+ggplot object

+}

+\description{

+add subview to mainview for ggplot2 objects

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,21 @@

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

+% Please edit documentation in R/ggtree.R

+\name{theme_transparent}

+\alias{theme_transparent}

+\title{theme_transparent}

+\usage{

+theme_transparent(...)

+}

+\arguments{

+\item{...}{additional parameter to tweak the theme}

+}

+\value{

+ggplot object

+}

+\description{

+transparent background theme

+}

+\author{

+Guangchuang Yu

+}

+