@@ -1,5 +1,7 @@

 CHANGES IN VERSION 1.7.4

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

+ o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>

+   + https://github.com/GuangchuangYu/ggtree/issues/98

  o groupOTU method now accept 'overlap = c("overwrite", "origin", "abandon")' parameter <2016-11-16, Wed>

    + https://groups.google.com/forum/#!topic/bioc-ggtree/Q4LnwoTf1DM

@@ -18,7 +18,7 @@ as.binary.phylo <- function(tree, ...) {

         cat("The input tree is already binary...\n")

         invisible(tree)

     }

-    

+

     polyNode <- tree$edge[,1] %>% table %>% '>'(2) %>%

         which %>% names %>% as.numeric

@@ -35,7 +35,7 @@ as.binary.phylo <- function(tree, ...) {

             idx <- idx[-1]

         }

     }

-        

+

     tree$Nnode <- tree$Nnode+ii

     tree$edge.length <- c(tree$edge.length, rep(0, ii))

     return(tree)

@@ -44,23 +44,23 @@ as.binary.phylo <- function(tree, ...) {

 ##' remove singleton

 ##'

-##' 

+##'

 ##' @title rm.singleton.newick

 ##' @param nwk newick file

-##' @param outfile output newick file 

+##' @param outfile output newick file

 ##' @return tree text

 ##' @importFrom magrittr %<>%

 ##' @importFrom magrittr add

 ##' @importFrom ape write.tree

 ##' @author Guangchuang Yu \url{http://ygc.name}

-rm.singleton.newick <- function(nwk, outfile = NULL) {    

+rm.singleton.newick <- function(nwk, outfile = NULL) {

     tree <- readLines(nwk)

     ## remove singleton of tips

     nodePattern <- "\\w+:[\\.0-9Ee\\+\\-]+"

     singletonPattern.with.nodename <- paste0(".*(\\(", nodePattern, "\\)\\w+:[\\.0-9Ee\\+\\-]+).*")

     singletonPattern.wo.nodename <- paste0(".*(\\(", nodePattern, "\\):[\\.0-9Ee\\+\\-]+).*")

-    

+

     while(length(grep("\\([^,]+\\)", tree)) > 0) {

         singleton <- gsub(singletonPattern.with.nodename, "\\1", tree)

         if (singleton == tree) {

@@ -71,11 +71,11 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {

         }

         tip <- gsub("\\((\\w+).*", "\\1", singleton)

-        

+

         len1 <- gsub(".*[^\\.0-9Ee\\+\\-]+([\\.0-9Ee\\+\\-]+)", "\\1", singleton)

         len2 <- gsub(".*:([\\.0-9Ee\\+\\-]+)\\).*", "\\1", singleton)

         len <- as.numeric(len1) + as.numeric(len2)

-        

+

         tree <- gsub(singleton, paste0(tip, ":", len), tree, fixed = TRUE)

     }

@@ -95,7 +95,7 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {

         tree$edge.length[sidx] %<>% add(., tree$edge.length[idx])

         tree$edge.length <- tree$edge.length[-idx]

     }

-    

+

     if (!is.null(outfile)) {

         write.tree(tree, file=outfile)

     }

@@ -117,12 +117,12 @@ fortify.beast <- function(model, data,

     df    <- fortify(phylo, layout=layout, branch.length=branch.length,

                      ladderize=ladderize, right=right, mrsd = mrsd, ...)

-    

+

     stats <- model@stats

     scn <- colnames(stats)

     scn <- scn[scn != 'node']

-    

+

     for (cn in scn) {

         if (cn %in% colnames(df)) {

             colnames(stats)[colnames(stats) == cn] <- paste0(cn, "_")

@@ -151,7 +151,7 @@ fortify.beast <- function(model, data,

             }

             next

         }

-        

+

         len <- sapply(stats[,ii], length)

         if ( all(len == 1) ) {

             stats[, ii] %<>% unlist %>% as.character %>% as.numeric

@@ -181,31 +181,31 @@ fortify.beast <- function(model, data,

                 } else {

                     return(paste0('{', paste0(y, collapse = ','), '}'))

                 }

-            })  

+            })

         }

     }

-            

-      

+

+

     cn <- colnames(stats)

     lo <- cn[grep("_lower", cn)]

     hi <- gsub("lower$", "upper", lo)

     rid <- gsub("_lower$", "", lo)

-    

+

     for (i in seq_along(rid)) {

         stats[, rid[i]] <- paste0("[", stats[, lo[i]], ",", stats[, hi[i]], "]")

         stats[is.na(stats[, lo[i]]), rid[i]] <- NA

     }

-    

+

     idx   <- match(df$node, stats$node)

     stats <- stats[idx,]

     cn_stats <- colnames(stats)

     stats <- stats[, cn_stats != "node"]

-    

+

     df <- cbind(df, stats)

     if (is(stats, "data.frame") == FALSE) {

         colnames(df)[colnames(df) == "stats"] <- cn_stats[cn_stats != "node"]

     }

-    

+

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

     append_extraInfo(df, model)

@@ -235,7 +235,7 @@ fortify.codeml <- function(model, data,

                           "rst.branch.length",

                           colnames(dNdS)[-c(1,2)])

                         )

-    

+

     if (length == "rst.branch.length") {

         phylo <- get.tree(model@rst)

     } else {

@@ -244,14 +244,14 @@ fortify.codeml <- function(model, data,

         }

         phylo <- set_branch_length(model@mlc, length)

     }

-    

+

     df <- fortify(phylo, data, layout, ladderize, right,

                   branch.length=length, mrsd=mrsd, ...)

-    

+

     res <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

     df <- merge_phylo_anno.paml_rst(res, model@rst)

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

-    

+

     append_extraInfo(df, model)

 }

@@ -269,10 +269,10 @@ fortify.codeml_mlc <- function(model, data,

                                ...) {

     phylo <- set_branch_length(model, branch.length)

-        

+

     df <- fortify(phylo, data, layout, ladderize, right,

                   branch.length=branch.length, mrsd=mrsd, ...)

-    

+

     dNdS <- model@dNdS

     df <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

@@ -290,12 +290,12 @@ merge_phylo_anno.codeml_mlc <- function(df, dNdS, ndigits = NULL) {

             }

         }

     }

-    

+

     res <- merge(df, dNdS,

                  by.x  = c("node", "parent"),

                  by.y  = c("node", "parent"),

                  all.x = TRUE)

-    

+

     res[match(df$node, res$node),]

 }

@@ -309,7 +309,7 @@ fortify.codeml_mlc_ <- function(model, data,

 }

-    

+

 ##' @method fortify paml_rst

 ##' @export

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

@@ -354,13 +354,13 @@ fortify.jplace <- function(model, data,

     df <- scaleY(model@phylo, df, yscale, layout, ...)

-    append_extraInfo(df, model)    

+    append_extraInfo(df, model)

 }

 scaleY <- function(phylo, df, yscale, layout, ...) {

     if (yscale == "none") {

         return(df)

-    } 

+    }

     if (! yscale %in% colnames(df)) {

         warning("yscale is not available...\n")

         return(df)

@@ -375,7 +375,7 @@ scaleY <- function(phylo, df, yscale, layout, ...) {

     } else {

         y <- getYcoord_scale_category(phylo, df, yscale, ...)

     }

-    

+

     df[, "y"] <- y

     return(df)

@@ -396,9 +396,10 @@ fortify.phylo4 <- function(model, data, layout="rectangular", yscale="none",

 ##' @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, ...)

+    res <- fortify.phylo4(model, data, layout, yscale="none", ladderize, right, mrsd, ...) # not apply yscale at this moment

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

-    cbind(res, tdata)

+    df <- cbind(res, tdata)

+    scaleY(as.phylo.phylo4(model), df, yscale, layout, ...)

 }

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

@@ -411,7 +412,7 @@ as.phylo.phylo4 <- function(phylo4) {

     phylo <- list(edge = edge,

                   edge.length = edge.length,

                   tip.label = tip.label)

-    

+

     node.id <- sort(unique(edge[,1]))

     node.id <- node.id[node.id != 0]

     node.label <- phylo4@label[node.id]

@@ -425,7 +426,7 @@ as.phylo.phylo4 <- function(phylo4) {

 ##' fortify a phylo to data.frame

 ##'

-##' 

+##'

 ##' @rdname fortify

 ##' @title fortify

 ##' @param model phylo object

@@ -442,7 +443,7 @@ as.phylo.phylo4 <- function(phylo4) {

 ##' @method fortify phylo

 ##' @export

 ##' @author Yu Guangchuang

-fortify.phylo <- function(model, data, layout="rectangular", 

+fortify.phylo <- function(model, data, layout="rectangular",

                           ladderize=TRUE, right=FALSE, mrsd=NULL, as.Date=FALSE, ...) {

     if (ladderize == TRUE) {

         tree <- ladderize(model, right=right)

@@ -456,7 +457,7 @@ fortify.phylo <- function(model, data, layout="rectangular",

             tree$edge.length <- NULL

         }

     }

-    

+

     df <- as.data.frame(tree, layout=layout, ...)

     idx <- is.na(df$parent)

     df$parent[idx] <- df$node[idx]

@@ -477,7 +478,7 @@ fortify.phylo <- function(model, data, layout="rectangular",

             }

         }

     }

-    

+

     if (!is.null(mrsd)) {

         df <- scaleX_by_time_from_mrsd(df, mrsd, as.Date)

     }

@@ -486,7 +487,7 @@ fortify.phylo <- function(model, data, layout="rectangular",

 ##' convert phylo to data.frame

 ##'

-##' 

+##'

 ##' @title as.data.frame

 ##' @param x phylo object

 ##' @param row.names omitted here

@@ -501,7 +502,7 @@ as.data.frame.phylo <- function(x, row.names, optional,

                                 layout="rectangular", ...) {

     if (layout == "unrooted") {

         return(layout.unrooted(x))

-    } 

+    }

     as.data.frame.phylo_(x, layout, ...)

 }

@@ -510,14 +511,14 @@ as.data.frame.phylo_ <- function(x, layout="rectangular",

     if (branch.length != 'none') {

         branch.length = "branch.length"

     }

-    

+

     tip.label <- x[["tip.label"]]

     Ntip <- length(tip.label)

     N <- getNodeNum(x)

-    

+

     edge <- as.data.frame(x[["edge"]])

     colnames(edge) <- c("parent", "node")

-    

+

     if (! is.null(x$edge.length)) {

         edge$length <- x$edge.length

         if (branch.length == "none") {

@@ -540,7 +541,7 @@ as.data.frame.phylo_ <- function(x, layout="rectangular",

         xpos <- getXcoord_no_length(x)

         ypos <- getYcoord(x)

     }

-    

+

     xypos <- data.frame(node=1:N, x=xpos, y=ypos)

     res <- merge(edge, xypos, by.x="node", by.y="node", all.y=TRUE)

@@ -588,7 +589,7 @@ fortify.apeBootstrap <- fortify.raxml

 ##' @method fortify multiPhylo

 ##' @export

-fortify.multiPhylo <-  function(model, data, layout="rectangular", 

+fortify.multiPhylo <-  function(model, data, layout="rectangular",

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

     df.list <- lapply(model, function(x) fortify(x, layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...))

@@ -600,9 +601,9 @@ fortify.multiPhylo <-  function(model, data, layout="rectangular",

     df <- do.call("rbind", df.list)

     df$.id <- rep(names(df.list), times=sapply(df.list, nrow))

     df$.id <- factor(df$.id, levels=names(df.list))

-    

+

     ## nNode <- sapply(df.list, nrow)

-    ## nNode2 <- cumsum(c(0, nNode[-length(nNode)])) 

+    ## nNode2 <- cumsum(c(0, nNode[-length(nNode)]))

     ## df$parent <- df$parent + rep(nNode2, times=nNode)

     return(df)

 }

@@ -615,7 +616,7 @@ fortify.phylip <- function(model, data, layout="rectangular",

     trees <- get.tree(model)

     fortify(trees, layout=layout, ladderize = ladderize, right=right, mrsd=mrsd, ...)

 }

-    

+

 ##' @method fortify r8s

 ##' @export

 fortify.r8s <- function(model, data, layout="rectangular",

@@ -659,7 +660,7 @@ fortify.phyloseq <- function(model, data, layout="rectangular",

     if ('Abundance' %in% colnames(dd)) {

         dd <- dd[dd$Abundance > 0, ]

     }

-    

+

     data <- merge(df, dd, by.x="label", by.y="OTU", all.x=TRUE)

     spacing <- 0.02

     idx <- with(data, sapply(table(node)[unique(node)], function(i) 1:i)) %>% unlist

@@ -669,7 +670,7 @@ fortify.phyloseq <- function(model, data, layout="rectangular",

     data[order(data$node, decreasing = FALSE), ]

 }

-                         

+

 ## fortify.cophylo <- function(model, data, layout="rectangular",

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

 ##     trees <- model$trees

@@ -2,9 +2,9 @@

 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-1.6.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.3-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-16443/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.4-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-16878/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />

-[![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--11--16-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--11--24-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)

@@ -18,7 +18,7 @@ Please cite the following article when using `ggtree`:

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted*

-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-273-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-272-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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

@@ -51,7 +51,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-16443/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-16878/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

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

          |                                                                                    *        |