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

 Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-Version: 1.5.14

+Version: 1.5.15

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.

@@ -165,7 +165,6 @@ importFrom(ape,read.tree)

 importFrom(ape,reorder.phylo)

 importFrom(ape,which.edge)

 importFrom(ape,write.tree)

-importFrom(ggplot2,"%+replace%")

 importFrom(ggplot2,GeomCurve)

 importFrom(ggplot2,GeomLabel)

 importFrom(ggplot2,GeomPoint)

@@ -214,6 +213,7 @@ importFrom(ggplot2,theme_bw)

 importFrom(ggplot2,xlab)

 importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

+importFrom(ggplot2,ylim)

 importFrom(grDevices,col2rgb)

 importFrom(grDevices,colorRampPalette)

 importFrom(grDevices,rgb)

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

+CHANGES IN VERSION 1.5.15

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

+ o check.aes for layers defined in ggtree <2016-10-07, Fri>

+ o recalculate 'angle' when collapse, expand and rotate clade <2016-10-06, Thu>

+   + https://github.com/GuangchuangYu/ggtree/issues/78

+

 CHANGES IN VERSION 1.5.14

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

  o subset tip in geom_tiplab2 <2016-10-05, Wed>

@@ -75,6 +75,9 @@ collapse <- function(tree_view=NULL, node) {

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

+    ii <- which(!is.na(df$x))

+    df$angle[ii] <- calculate_angle(df[ii,])$angle

+    

     tree_view$data <- df

     clade <- paste0("clade_", node)

     attr(tree_view, clade) <- sp.df

@@ -121,7 +124,7 @@ expand <- function(tree_view=NULL, node) {

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

-    tree_view$data <- df

+    tree_view$data <- calculate_angle(df)

     attr(tree_view, clade) <- NULL

     tree_view

 }

@@ -156,7 +159,8 @@ rotate <- function(tree_view=NULL, node) {

     if (pnode != node && !is.na(pnode)) {

         df[df$node == pnode, "y"] <- mean(df[df$parent == pnode, "y"])

     }

-    tree_view$data <- df

+

+    tree_view$data <- calculate_angle(df)

     tree_view

 }

@@ -218,6 +222,7 @@ flip <- function(tree_view=NULL, node1, node2) {

     currentNode <- currentNode[!currentNode %in% anc]

     tree_view$data <- re_assign_ycoord_df(df, currentNode)

+    tree_view$data <- calculate_angle(tree_view$data)

     tree_view

 }

@@ -281,7 +286,7 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

-    tree_view$data <- df

+    tree_view$data <- calculate_angle(df)

     tree_view

 }

@@ -44,7 +44,8 @@ geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend

                   extend=extend,

                   extendto=extendto,

                   direction=1, 

-                  na.rm = na.rm)

+                  na.rm = na.rm),

+    check.aes = FALSE

   )

   l2 <- layer(

     stat=StatBalance,

@@ -61,7 +62,8 @@ geom_balance <- function(node, fill="steelblue", color='white', alpha=.5, extend

                   extend=extend,

                   extendto=extendto,

                   direction=2,

-                  na.rm = na.rm)

+                  na.rm = na.rm),

+    check.aes = FALSE

   )

   return(c(l1,l2))

 }

@@ -113,7 +115,8 @@ stat_balance <- function(mapping=NULL, data=NULL, geom="rect",

                   extend=extend,

                   extendto=extendto,

                   direction=1,

-                  ...)

+                  ...),

+    check.aes = FALSE

   )

   l2 <- layer(

     stat=StatBalance,

@@ -130,7 +133,8 @@ stat_balance <- function(mapping=NULL, data=NULL, geom="rect",

                   extend=extend,

                   extendto=extendto,

                   direction=2,

-                  ...)

+                  ...),

+    check.aes = FALSE

   )

   return(c(l1,l2))

 }

@@ -205,4 +209,4 @@ get_balance_position_ <- function(data, node, direction) {

              xmax = max(x),

              ymin=min(y)-0.5,

              ymax=max(y)+0.5)

-}

\ No newline at end of file

+}

@@ -128,7 +128,8 @@ stat_cladeText <- function(mapping=NULL, data=NULL,

                       align  = align,

                       na.rm  = na.rm,

                       parse  = parse,

-                      ...)

+                      ...),

+          check.aes = FALSE

           )

 }

@@ -155,9 +156,9 @@ stat_cladeBar <- function(mapping=NULL, data=NULL,

                       offset=offset,

                       align=align,

                       na.rm=na.rm,

-                      ...)

+                      ...),

+          check.aes = FALSE

           )

-

 }

 StatCladeText <- ggproto("StatCladeText", Stat,

@@ -39,7 +39,8 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5, extend=0, extendto=NU

                       alpha=alpha,

                       extend=extend,

                       extendto=extendto,

-                      na.rm = na.rm)

+                      na.rm = na.rm),

+        check.aes = FALSE

     )

 }

@@ -66,7 +66,8 @@ geom_label2 <- function(mapping = NULL, data = NULL,

             label.size = label.size,

             na.rm = na.rm,

             ...

-        )

+        ),

+        check.aes = FALSE

     )

 }

@@ -125,7 +125,8 @@ geom_point2 <- function(mapping = NULL, data = NULL,

         params = list(

             na.rm = na.rm,

             ...

-        )

+        ),

+        check.aes = FALSE

     )

 }

@@ -67,7 +67,8 @@ geom_segment2 <- function(mapping = NULL, data = NULL,

             lineend = lineend,

             na.rm = na.rm,

             ...

-        )

+        ),

+        check.aes = FALSE

     )

 }

@@ -97,7 +97,8 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       barextend=barextend,

                       na.rm=na.rm,

                       parse=parse,

-                      ...)

+                      ...),

+          check.aes = FALSE

           )

 }

@@ -132,7 +133,8 @@ stat_stripBar <- function(mapping=NULL, data=NULL,

                       align=align,

                       barextend=barextend,

                       na.rm=na.rm,

-                      ...)

+                      ...),

+          check.aes = FALSE

           )

 }

@@ -30,7 +30,8 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {

                         taxa2 = taxa2,

                         curvature = curvature,

                         na.rm = na.rm,

-                        ...)

+                        ...),

+          check.aes = FALSE

           )

 }

@@ -22,7 +22,8 @@

 ##' \link[ggplot2]{geom_text}

 ##' @author Guangchuang Yu

 geom_text2 <- function(mapping = NULL, data = NULL,

-                       position = "identity", parse = FALSE, na.rm=TRUE, show.legend = NA, inherit.aes = TRUE,

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

+                       inherit.aes = TRUE,

                        ..., nudge_x = 0, nudge_y = 0, check_overlap = FALSE) {

     if (!missing(nudge_x) || !missing(nudge_y)) {

@@ -53,7 +54,8 @@ geom_text2 <- function(mapping = NULL, data = NULL,

           check_overlap = check_overlap,

           na.rm = na.rm,

           ...

-        )

+        ),

+        check.aes = FALSE

     )

 }

@@ -91,7 +91,8 @@ geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {

 geom_tipsegment <- function(mapping=NULL, data=NULL,

                             geom=GeomSegmentGGtree, position = "identity",

                             offset,  ...,

-                            show.legend=NA, inherit.aes=FALSE, na.rm=TRUE) {

+                            show.legend=NA, inherit.aes=FALSE,

+                            na.rm=TRUE) {

     default_aes <- aes_(x=~x, y=~y)

     if (is.null(mapping)) {

@@ -109,7 +110,8 @@ geom_tipsegment <- function(mapping=NULL, data=NULL,

           inherit.aes = inherit.aes,

           params = list(offset = offset,

                         na.rm = na.rm,

-                        ...)

+                        ...),

+          check.aes = FALSE

           )

 }

@@ -46,7 +46,8 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit

                    params=list(layout = layout,

                                lineend = lineend,

                                na.rm = na.rm,

-                          ...)

+                               ...),

+                   check.aes = FALSE

                    ),

              layer(data=data,

                    mapping=mapping,

@@ -58,7 +59,8 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit

                    params=list(layout = layout,

                                lineend = lineend,

                                na.rm = na.rm,

-                               ...)

+                               ...),

+                   check.aes = FALSE

                    )

              )

     } else if (layout %in% c("slanted", "radial", "unrooted")) {

@@ -72,7 +74,8 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit

               params=list(layout = layout,

                           lineend = lineend,

                           na.rm = na.rm,

-                          ...)

+                          ...),

+              check.aes = FALSE

               )

     }

 }

@@ -21,7 +21,7 @@

 ##' @importFrom ggplot2 ylab

 ##' @importFrom ggplot2 annotate

 ##' @importFrom ggplot2 scale_x_reverse

-##' @importFrom ggplot2 scale_y_continuous

+##' @importFrom ggplot2 ylim

 ##' @importFrom ggplot2 coord_flip

 ##' @importFrom ggplot2 coord_polar

 ##' @export

@@ -86,7 +86,7 @@ ggtree <- function(tr,

         p <- layout_circular(p)

         ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6

         ## and also have some space for tree scale (legend)

-        p <- p + scale_y_continuous(limits=c(0, max(p$data$y)+1))

+        p <- p + ylim(0, NA) 

     } else if (layout == "fan") {

         p <- layout_fan(p, open.angle)

     }

@@ -74,9 +74,9 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     dd$width <- width

     if (is.null(color)) {

-        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value, width=width), inherit.aes=FALSE)

+        p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)

     } else {

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

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

     }

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

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

@@ -12,7 +12,7 @@

 ##' @return tree view with insets

 ##' @export

 ##' @author Guangchuang Yu

-inset <- function(tree_view, insets, width=0.05, height=0.05, hjust=0, vjust=0, x="node") {

+inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x="node") {

     df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

@@ -25,6 +25,7 @@ layout_circular <- function(treeview) {

 ##' @param treeview tree view

 ##' @param angle angle

 ##' @return updated tree view

+##' @importFrom ggplot2 scale_y_continuous

 ##' @export

 ##' @author Guangchuang Yu

 open_tree <- function(treeview, angle) {

@@ -36,7 +37,7 @@ open_tree <- function(treeview, angle) {

     N <- nrow(p$data)

     idx <- match(1:N, order(p$data$y))

     NN <- N *(1+angle/(360-angle))

-    angle <- 360/(3+NN) * (1:N+1)

+    angle <- 360/(2+NN) * (1:N+1)

     angle <- angle[idx]

     p$data$angle <- angle

     return(p)

@@ -558,15 +558,7 @@ as.data.frame.phylo_ <- function(x, layout="rectangular",

     res <- calculate_branch_mid(res)

     ## ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle

-    ## ## if (layout == "circular") {

-    ## idx <- match(1:N, order(res$y))

-    ## ## angle <- -360/(3+N) * (1:N+1)

-    ## angle <- 360/(3+N) * (1:N+1)

-    ## angle <- angle[idx]

-    ## ## res$angle <- angle + 90

-    ## res$angle <- angle

-    ## } 

-    res$angle <- 360/(diff(range(res$y)) + 1) * res$y

+    res <- calculate_angle(res)

     return(res)

 }

@@ -692,3 +684,9 @@ fortify.phyloseq <- function(model, data, layout="rectangular",

 ##     ggplot(df) + geom_tree()

 ## }

+

+

+calculate_angle <- function(data) {

+    data$angle <- 360/(diff(range(data$y)) + 1) * data$y

+    return(data)

+}

@@ -8,7 +8,6 @@

 ##' @importFrom ggplot2 theme_bw

 ##' @importFrom ggplot2 theme

 ##' @importFrom ggplot2 element_blank

-##' @importFrom ggplot2 %+replace%

 ##' @importFrom ggplot2 xlab

 ##' @importFrom ggplot2 ylab

 ##' @export

@@ -21,12 +20,12 @@

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

     list(xlab(NULL),

          ylab(NULL),

-	 theme_tree2_internal() %+replace%

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

-            axis.line.x = element_blank(),

-            axis.text.x = element_blank(),

-            axis.ticks.x = element_blank(),

-            ...)

+	 theme_tree2_internal() + 

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

+               axis.line.x = element_blank(),

+               axis.text.x = element_blank(),

+               axis.ticks.x = element_blank(),

+               ...)

 	 )

 }

@@ -41,7 +40,6 @@ theme_tree <- function(bgcolor="white", fgcolor="black", ...) {

 ##' @importFrom ggplot2 theme

 ##' @importFrom ggplot2 element_blank

 ##' @importFrom ggplot2 element_line

-##' @importFrom ggplot2 %+replace%

 ##' @importFrom ggplot2 element_rect

 ##' @export

 ##' @return updated ggplot object with new theme

@@ -65,18 +63,18 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",

                                  axis.line.y=element_blank(),

                                  axis.ticks.y=element_blank(),

                                  axis.text.y=element_blank(),...) {

-    theme_bw() %+replace%

-    theme(legend.position=legend.position,

-          panel.grid.minor=panel.grid.minor,

-          panel.grid.major=panel.grid.major,

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

-          panel.border=panel.border,

-          ## axis.line=element_line(color=fgcolor),

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

-          axis.line.y=axis.line.y,

-          axis.ticks.y=axis.ticks.y,

-          axis.text.y=axis.text.y,

-          ...)

+    theme_bw() + 

+        theme(legend.position=legend.position,

+              panel.grid.minor=panel.grid.minor,

+              panel.grid.major=panel.grid.major,

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

+              panel.border=panel.border,

+              ## axis.line=element_line(color=fgcolor),

+              axis.line.x=element_line(color=fgcolor),

+              axis.line.y=axis.line.y,

+              axis.ticks.y=axis.ticks.y,

+              axis.text.y=axis.text.y,

+              ...)

 }

 ##' transparent background theme

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

 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

 ===========================================================================================================================

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.14-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-14686/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.15-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-14686/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--05-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--10--07-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

@@ -4,7 +4,7 @@

 \alias{inset}

 \title{inset}

 \usage{

-inset(tree_view, insets, width = 0.05, height = 0.05, hjust = 0,

+inset(tree_view, insets, width = 0.1, height = 0.1, hjust = 0,

   vjust = 0, x = "node")

 }

 \arguments{

@@ -112,7 +112,7 @@ inset(p, bars)

 The sizes of the insets can be ajusted by the paramter *width* and *height*.

 ```{r}

-inset(p, bars, width=.03, height=.06)

+inset(p, bars, width=.06, height=.1)

 ```

 Users can set the color via the parameter *color*. The *x* position can be one of 'node' or 'branch' and can be adjusted by the parameter *hjust* and *vjust* for horizontal and vertical adjustment respecitvely.

@@ -121,7 +121,7 @@ Users can set the color via the parameter *color*. The *x* position can be one o

 ```{r}

 bars2 <- nodebar(dat, cols=1:4, position='dodge',

                  color=c(a='blue', b='red', c='green', d='cyan'))

-p2 <- inset(p, bars2, x='branch', width=.03, vjust=-.3)

+p2 <- inset(p, bars2, x='branch', width=.06, vjust=-.3)

 print(p2)

 ```

@@ -157,7 +157,7 @@ bx <- lapply(d, function(y) {

     ggplot(dd, aes(x=1, y=y))+geom_boxplot() + ylim(ylim) + theme_inset()

 })

 names(bx) <- 1:15

-inset(p, bx, width=.03, height=.1, hjust=-.05)

+inset(p, bx, width=.06, height=.2, hjust=-.05)

 ```

@@ -167,7 +167,7 @@ After annotating with insets, users can further annotate the tree with another l

 p2 <- inset(p, bars2, x='branch', width=.03, vjust=-.4)

 p2 <- inset(p2, pies, x='branch', vjust=.4)

 bx2 <- lapply(bx, function(g) g+coord_flip())

-inset(p2, bx2, width=.2, height=.03, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)

+inset(p2, bx2, width=.4, height=.06, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)

 ```

 ## Annotate with image files

@@ -141,7 +141,7 @@ ggtree(chiroptera, aes(color=group), layout='circular') + geom_tiplab(size=1, ae

 In this example, we first build a tree based on the iris data, then grouping the tree based on different spacies.

-```{r fig.width=20, fig.height=20, fig.align="center", warning=FALSE}

+#```{r fig.width=20, fig.height=20, fig.align="center", warning=FALSE}

 data(iris)

 rn <- paste0(iris[,5], "_", 1:150)

 rownames(iris) <- rn

@@ -157,7 +157,7 @@ ggtree(tree_iris, aes(color=group)) +

     scale_color_manual(values=cols, breaks=1:3,

                        labels=c("Setosa", "Versicolor", "Virginica")) +

     theme(legend.position="right")

-```		

+#```		

 -->