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

 Package: ggtree

 Type: Package

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

-Version: 1.5.1

+Version: 1.5.2

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -16,6 +16,7 @@ S3method(fortify,phangorn)

 S3method(fortify,phylip)

 S3method(fortify,phylo)

 S3method(fortify,phylo4)

+S3method(fortify,phylo4d)

 S3method(fortify,phyloseq)

 S3method(fortify,r8s)

 S3method(fortify,raxml)

@@ -1,3 +1,8 @@

+CHANGES IN VERSION 1.5.2

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

+ o supports phylo4d object <2016-05-10, Tue>

+   + https://github.com/GuangchuangYu/ggtree/issues/47

+ 

 CHANGES IN VERSION 1.5.1

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

  o update vignettes <2016-05-10, Tue>

@@ -44,15 +44,17 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     start <- max(df$x) + offset

     dd <- data

-    dd$lab <- rownames(dd)

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

+    ## dd$lab <- rownames(dd)

+    lab <- df$label[order(df$y)]

+    dd <- dd[lab, ]

     dd$y <- sort(df$y)

-    

+    dd$lab <- lab

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

     dd <- gather(dd, variable, value, -c(lab, y))

-    

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

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

+

+    i <- which(dd$value == "")

+    if (length(i) > 0) {

+        dd$value[i] <- NA

     }

     if (is.null(colnames_level)) {

         dd$variable <- factor(dd$variable, levels=colnames(data))

@@ -87,7 +89,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     }

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

-    p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))

+    ## p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))

     attr(p2, "mapping") <- mapping

     return(p2)

@@ -412,6 +412,15 @@ fortify.phylo4 <- function(model, data, layout="rectangular", yscale="none",

     scaleY(phylo, df, yscale, layout, ...)

 }

+##' @method fortify phylo4d

+##' @export

+fortify.phylo4d <- function(model, data, layout="rectangular", yscale="none",

+                            ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {

+    res <- fortify.phylo4(model, data, layout, yscale, ladderize, right, mrsd, ...)

+    tdata <- model@data[match(res$node, rownames(model@data)), , drop=FALSE]

+    cbind(res, tdata)

+}

+

 as.phylo.phylo4 <- function(phylo4) {

     edge <- phylo4@edge

     edge <- edge[edge[,1] != 0, ]