1. ggtree
  2. Commit 7f332d206029e123f26e2643bfec8c2a534fc241
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update docs

guangchuang yu authored on 31/07/2017 10:10:37
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R/jplace.R
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-## ##' read jplace file
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-## ##'
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-## ##'
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-## ##' @title read.jplace
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-## ##' @param file jplace file
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-## ##' @return \code{jplace} instance
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-## ##' @importFrom jsonlite fromJSON
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-## ##' @export
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-## ##' @author ygc
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-## ##' @examples
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-## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
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-## ##' read.jplace(jp)
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-## read.jplace <- function(file) {
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-##     fields <- tree <- placements <- NULL
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-##     version <- metadata <- NULL
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-##     with(fromJSON(file),
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-##          new("jplace",
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-##              fields     = fields,
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-##              treetext   = tree,
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-##              phylo      = jplace_treetext_to_phylo(tree),
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-##              placements = placements,
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-##              version    = version,
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-##              metadata   = metadata,
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-##              file       = filename(file)
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-##              )
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-##          )
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-## }
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-
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-
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-
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-## ##' @rdname scale_color-methods
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-## ##' @exportMethod scale_color
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-## setMethod("scale_color", signature(object="jplace"),
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-##           function(object, by, ...) {
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-##               scale_color_(object, by, ...)
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-##           })
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-
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-
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-
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-
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-## ##' get.treeinfo method
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-## ##'
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-## ##'
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-## ##' @docType methods
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-## ##' @name get.treeinfo
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-## ##' @rdname get.treeinfo-methods
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-## ##' @aliases get.treeinfo,jplace,ANY-method
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-## ##' @exportMethod get.treeinfo
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-## ##' @author Guangchuang Yu \url{http://ygc.name}
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-## ##' @usage get.treeinfo(object, layout, ladderize, right, ...)
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-## ##' @examples
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-## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
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-## ##' jp <- read.jplace(jp)
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-## ##' get.treeinfo(jp)
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-## setMethod("get.treeinfo", signature(object = "jplace"),
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-##           function(object, layout="phylogram",
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-##                    ladderize=TRUE, right=FALSE, ...) {
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-##               get.treeinfo.jplace(object, layout,
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-##                                   ladderize, right, ...)
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-##           }
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-##           )
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-
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-
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-## ##' get.treetext method
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-## ##'
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-## ##'
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-## ##' @docType methods
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-## ##' @name get.treetext
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-## ##' @rdname get.treetext-methods
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-## ##' @aliases get.treetext,jplace,ANY-method
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-## ##' @exportMethod get.treetext
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-## ##' @author Guangchuang Yu \url{http://ygc.name}
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-## ##' @usage get.treetext(object, ...)
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-## ##' @examples
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-## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
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-## ##' jp <- read.jplace(jp)
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-## ##' get.treetext(jp)
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-## setMethod("get.treetext", signature(object = "jplace"),
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-##           function(object, ...) {
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-##               get.treetext.jplace(object, ...)
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-##           }
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-##           )
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-
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-
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-## ##' get.fields method
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-## ##'
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-## ##'
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-## ##' @docType methods
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-## ##' @name get.fields
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-## ##' @rdname get.fields-methods
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-## ##' @aliases get.fields,jplace,ANY-method
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-## ##' @exportMethod get.fields
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-## ##' @author Guangchuang Yu \url{http://ygc.name}
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-## ##' @usage get.fields(object, ...)
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-## ##' @examples
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-## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
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-## ##' jp <- read.jplace(jp)
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-## ##' get.fields(jp)
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-## setMethod("get.fields", signature(object = "jplace"),
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-##           function(object, ...) {
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-##               get.fields.tree(object)
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-##           }
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-##           )
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-
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-## ##' get.placement method
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-## ##'
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-## ##'
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-## ##' @docType methods
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-## ##' @name get.placements
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-## ##' @rdname get.placements-methods
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-## ##' @aliases get.placements,jplace,ANY-method
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-## ##' @exportMethod get.placements
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-## ##' @author Guangchuang Yu \url{http://ygc.name}
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-## ##' @usage get.placements(object, by, ...)
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-## ##' @examples
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-## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")
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-## ##' jp <- read.jplace(jp)
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-## ##' get.placements(jp, by="all")
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-## setMethod("get.placements", signature(object = "jplace"),
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-##           function(object, by="best", ...) {
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-
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-##               placements <- object@placements
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-##               place <- placements[,1]
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-
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-##               ids <- NULL
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-##               if (length(placements) == 2) {
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-##                   ids <- sapply(placements[,2], function(x) x[1])
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-##                   names(place) <- ids
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-##               }
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-##               if (by == "best") { ## best hit
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-##                   place <- lapply(place, function(x) {
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-##                       if (is(x, "data.frame") || is(x, "matrix")) {
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-##                           if (nrow(x) == 1) {
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-##                               return(x)
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-##                           }
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-##                           ## http://astrostatistics.psu.edu/su07/R/html/base/html/all.equal.html
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-##                           ## due to precision, number are identical maynot be equal, so use all.equal which can test nearly equal number
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-##                           ## if not equals, the output is a descript string of the differences
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-##                           idx <- sapply(2:nrow(x), function(i) all.equal(x[1,2], x[i,2]))
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-##                           if (any(idx == TRUE)) {
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-##                               return(x[c(1, which(idx==TRUE)+1),])
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-##                           } else {
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-##                               return(x[1,])
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-##                           }
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-
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-##                       } else {
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-##                           ## if only 1 row, it may stored as vector
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-##                           ## the edge number, for example 523 can be 523.0000 due to R stored number as real number
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-##                           ## be careful in mapping edge number.
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-##                           return(x)
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-##                       }
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-##                   })
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-
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-##               }
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-
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-##               place.df <- do.call("rbind", place)
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-##               row.names(place.df) <- NULL
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-##               if (!is.null(ids)) {
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-##                   nn <- rep(ids, sapply(place, function(x) {
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-##                       nr <- nrow(x)
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-##                       if (is.null(nr))
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-##                           return(1)
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-##                       return(nr)
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-##                   }))
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-##                   place.df <- data.frame(name=nn, place.df)
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-##                   colnames(place.df) <- c("name", object@fields)
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-##               } else {
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-##                   colnames(place.df) <- object@fields
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-##               }
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-##               res <- as.data.frame(place.df, stringsAsFactor=FALSE)
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-
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-##               ## res[] <- lapply(res, as.character)
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-##               ## for (i in 1:ncol(res)) {
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-##               ##     if (all(grepl("^[0-9\\.e]+$", res[,i]))) {
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-##               ##         res[,i] <- as.numeric(res[,i])
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-##               ##     }
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-##               ## }
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-##               return(res)
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-##           })
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-
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-
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-## get.treetext.jplace <- function(object, ...) {
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-##     object@treetext
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-## }
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-
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-## get.fields.jplace <- function(object, ...) {
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-##     object@fields
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-## }
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-
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-## get.treeinfo.jplace <- function(object, layout,
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-##                                 ladderize, right, ...) {
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-##     extract.treeinfo.jplace(object, layout,
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-##                             ladderize, right, ...)
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-## }
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-
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-## ##' generate jplace file
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-## ##'
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-## ##'
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-## ##' @title write.jplace
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-## ##' @param nwk tree in newick format
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-## ##' @param data annotation data
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-## ##' @param outfile jplace output file
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-## ##' @return jplace file
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-## ##' @export
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-## ##' @author ygc
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-## ##' @examples
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-## ##' tree <- system.file("extdata", "pa.nwk", package="ggtree")
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-## ##' data <- read.csv(system.file("extdata", "pa_subs.csv", package="ggtree"),
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-## ##'                 stringsAsFactor=FALSE)
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-## ##' outfile <- tempfile()
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-## ##' write.jplace(tree, data, outfile)
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-## write.jplace <- function(nwk, data, outfile) {
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-##     out <- file(outfile, "w")
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-##     data[] = lapply(data, as.character) ## remove factor
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-##     writeLines("{", out)
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-##     writeLines(paste0('\t"tree": "', readLines(nwk), '",'), out)
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-##     writeLines('\t"placements": [', out)
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-##     for (i in 1:nrow(data)) {
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-##         writeLines(paste0('\t{"p":["', paste(data[i,], collapse = '", "'), '"]}'), out, sep="")
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-##         if (i != nrow(data)) {
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-##             writeLines(',', out)
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-##         }
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-##     }
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-##     writeLines('],', out)
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-##     writeLines('\t"metadata": {"info": "generated by ggtree package"},',
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-##                out)
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-##     writeLines('\t"version": 2,', out)
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-##     writeLines(paste0('\t"fields": [', '"',
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-##                       paste(colnames(data), collapse='", "'),
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-##                       '"'),
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-##                out)
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-##     writeLines('\t]\n}', out)
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-##     close(out)
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-## }
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-
README.md
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![](https://img.shields.io/badge/release%20version-1.8.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.2-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) [![](https://img.shields.io/badge/download-17269/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/release%20version-1.8.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.3-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) [![](https://img.shields.io/badge/download-17269/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![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-2017--07--26-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)
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+[![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-2017--07--31-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)
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 [![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) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
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@@ -27,7 +27,7 @@ Please cite the following article when using `ggtree`:
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 **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***. 2017, 8(1):28-36.
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-[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-350-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-29-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-349-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-29-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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 ------------------------------------------------------------------------
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docs/documentation/index.html
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@@ -384,6 +384,8 @@
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 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
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 <li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>
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 <li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a> <i class="fa fa-arrow-left"></i> The Molecular Ecologist</li>
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+<li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
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+<li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
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 </ul>
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 </div>
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 <div id="tree-annotation" class="section level3">
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 <li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/">facet_plot: a general solution to associate data with phylogenetic tree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/">align genomic features with phylogenetic tree</a></li>
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+<li><a href="https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree">ggjoy facet with ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree panel</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>
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 </ul>
docs/documentation/index.rmd
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 + [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)
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 + [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)
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 + [Phylogenetic trees in R using ggtree](http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/) <i class="fa fa-arrow-left"></i> The Molecular Ecologist
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++ [Growing a ggtree](https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration)
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++ [Growing a ggtree - part 2, adding tip shapes](https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2)
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 ### <i class="fa fa-angle-double-right"></i> Tree annotation
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 + [identify method for ggtree](https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree)
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 + [facet_plot: a general solution to associate data with phylogenetic tree](https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/)
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 + [align genomic features with phylogenetic tree](https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/)
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++ [ggjoy facet with ggtree](https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree)
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 + [xlim_tree: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/)
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 + [add layer to specific panel of facet_plot output](https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/)
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docs/documentation/index.xml
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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       <guid>https://guangchuangyu.github.io/ggtree/documentation/</guid>
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-      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)   </description>
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+      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist Growing a ggtree Growing a ggtree - part 2, adding tip shapes    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)   </description>
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 				<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
346 346 
 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
347 
-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.2-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17269/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
347 
+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17269/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
348 348 
 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
349 349 
 <div id="authors" class="section level2">
350 350 
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353 353 
 <div id="citation" class="section level2">
354 354 
 <h2><i class="fa fa-book"></i> Citation</h2>
355 355 
 <p>Please cite the following article when using <code>ggtree</code>:</p>
356 
-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-351-blue.svg?style=flat" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-29-blue.svg?style=flat" alt="citation" /></a></p>
356 
+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-349-blue.svg?style=flat" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-29-blue.svg?style=flat" alt="citation" /></a></p>
357 357 
 <p><strong>G Yu</strong>, 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. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p>
358 358 
 </div>
359 359 
 <div id="featured-articles" class="section level2">
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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       <guid>https://guangchuangyu.github.io/ggtree/documentation/</guid>
31 
-      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)   </description>
31 
+      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist Growing a ggtree Growing a ggtree - part 2, adding tip shapes    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)   </description>
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     <item>
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@@ -76,9 +76,9 @@ http://dx.doi.org/10.1111/2041-210X.12628
76 76
77 77 
       <guid>https://guangchuangyu.github.io/ggtree/tweets/</guid>
78 78 
       <description>Leave me a message on
79 
-Second post with an update on how to add tip shapes and colours to ggtree https://t.co/ezWF4TVQst
80 
-&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 Yes and no. No manual assignment =&amp;gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀
81 
-&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 I&amp;#39;d use ggtree from Bioconductor as you can really tailor all the fonts etc.</description>
79 
+Possible to combine #ggjoy with #ggtree ? My gg-fu is weak. #rstats #DataViz #JoyPlot https://t.co/4FICfER6Oa
80 
+&amp;mdash; Libby Megna (@LibbyMegna) July 29, 2017 Second post with an update on how to add tip shapes and colours to ggtree https://t.co/ezWF4TVQst
81 
+&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 Yes and no. No manual assignment =&amp;gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀</description>
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     </item>
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343 343
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 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
345 345 
 <p><font size="4"><strong>Leave me a message on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a></strong></font></p>
346 
-<p><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Second post with an update on how to add tip shapes and colours to ggtree <a href="https://t.co/ezWF4TVQst">https://t.co/ezWF4TVQst</a></p>&mdash; Anthony Underwood (@bioinformAnt) <a href="https://twitter.com/bioinformAnt/status/883301626022375424">July 7, 2017</a></blockquote>
346 
+<p><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Possible to combine <a href="https://twitter.com/hashtag/ggjoy?src=hash">#ggjoy</a> with <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> ? My gg-fu is weak. <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> <a href="https://twitter.com/hashtag/DataViz?src=hash">#DataViz</a> <a href="https://twitter.com/hashtag/JoyPlot?src=hash">#JoyPlot</a> <a href="https://t.co/4FICfER6Oa">https://t.co/4FICfER6Oa</a></p>&mdash; Libby Megna (@LibbyMegna) <a href="https://twitter.com/LibbyMegna/status/891144389715783680">July 29, 2017</a></blockquote>
347 
+<script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Second post with an update on how to add tip shapes and colours to ggtree <a href="https://t.co/ezWF4TVQst">https://t.co/ezWF4TVQst</a></p>&mdash; Anthony Underwood (@bioinformAnt) <a href="https://twitter.com/bioinformAnt/status/883301626022375424">July 7, 2017</a></blockquote>
347 348 
 <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Yes and no. No manual assignment =&gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀</p>&mdash; Anthony Underwood (@bioinformAnt) <a href="https://twitter.com/bioinformAnt/status/883246854695256064">July 7, 2017</a></blockquote>
348 349 
 <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">I&#39;d use ggtree from Bioconductor as you can really tailor all the fonts etc..<a href="https://t.co/NAcbFswGYB">https://t.co/NAcbFswGYB</a></p>&mdash; Susan Holmes (@SherlockpHolmes) <a href="https://twitter.com/SherlockpHolmes/status/877576023109390336">June 21, 2017</a></blockquote>
349 350 
 <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script><blockquote class="twitter-tweet"><p lang="en" dir="ltr">How phylogenies and associated heatmaps can be drawn using the <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> package in <a href="https://twitter.com/hashtag/R?src=hash">#R</a> <a href="https://t.co/rlBvGxUEBO">https://t.co/rlBvGxUEBO</a></p>&mdash; L. Rosaleny (@lorelai66) <a href="https://twitter.com/lorelai66/status/875594411584782337">June 16, 2017</a></blockquote>
docs/tweets/index.rmd
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12 12
13 13 
 ````{r echo=FALSE}
14 
+blogdown::shortcode('tweet', '891144389715783680')
14 15 
 blogdown::shortcode('tweet', '883301626022375424')
15 16 
 blogdown::shortcode('tweet', '883246854695256064')
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 blogdown::shortcode('tweet', '877576023109390336')
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19 19
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       <guid>https://guangchuangyu.github.io/ggtree/tweets/</guid>
21 21 
       <description>Leave me a message on
22 
-Second post with an update on how to add tip shapes and colours to ggtree https://t.co/ezWF4TVQst
23 
-&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 Yes and no. No manual assignment =&amp;gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀
24 
-&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 I&amp;#39;d use ggtree from Bioconductor as you can really tailor all the fonts etc.</description>
22 
+Possible to combine #ggjoy with #ggtree ? My gg-fu is weak. #rstats #DataViz #JoyPlot https://t.co/4FICfER6Oa
23 
+&amp;mdash; Libby Megna (@LibbyMegna) July 29, 2017 Second post with an update on how to add tip shapes and colours to ggtree https://t.co/ezWF4TVQst
24 
+&amp;mdash; Anthony Underwood (@bioinformAnt) July 7, 2017 Yes and no. No manual assignment =&amp;gt; randomly assigned colours. Even with manual spec ggtree is still much quicker than making fig by hand 😀</description>
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 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
50 50 
 <li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>
51 51 
 <li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a> <i class="fa fa-arrow-left"></i> The Molecular Ecologist</li>
52 
+<li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
53 
+<li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
52 54 
 </ul>
53 55 
 </div>
54 56 
 <div id="tree-annotation" class="section level3">
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63 65 
 <li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for ggtree</a></li>
64 66 
 <li><a href="https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/">facet_plot: a general solution to associate data with phylogenetic tree</a></li>
65 67 
 <li><a href="https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/">align genomic features with phylogenetic tree</a></li>
68 
+<li><a href="https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree">ggjoy facet with ggtree</a></li>
66 69 
 <li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree panel</a></li>
67 70 
 <li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>
68 71 
 </ul>
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44 44 
 + [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)
45 45 
 + [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)
46 46 
 + [Phylogenetic trees in R using ggtree](http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/) <i class="fa fa-arrow-left"></i> The Molecular Ecologist
47 
++ [Growing a ggtree](https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration)
48 
++ [Growing a ggtree - part 2, adding tip shapes](https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2)
47 49
48 50 
 ### <i class="fa fa-angle-double-right"></i> Tree annotation
49 51
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56 58 
 + [identify method for ggtree](https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree)
57 59 
 + [facet_plot: a general solution to associate data with phylogenetic tree](https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/)
58 60 
 + [align genomic features with phylogenetic tree](https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/)
61 
++ [ggjoy facet with ggtree](https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree)
59 62 
 + [xlim_tree: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/)
60 63 
 + [add layer to specific panel of facet_plot output](https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/)
61 64
site_src/content/index.html
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10 10 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
11 11 
 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
12 
-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.2-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17269/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
12 
+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17269/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
13 13 
 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
14 14 
 <div id="authors" class="section level2">
15 15 
 <h2><i class="fa fa-user"></i> Authors</h2>
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18 18 
 <div id="citation" class="section level2">
19 19 
 <h2><i class="fa fa-book"></i> Citation</h2>
20 20 
 <p>Please cite the following article when using <code>ggtree</code>:</p>
21 
-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-351-blue.svg?style=flat" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-29-blue.svg?style=flat" alt="citation" /></a></p>
21 
+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-349-blue.svg?style=flat" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-29-blue.svg?style=flat" alt="citation" /></a></p>
22 22 
 <p><strong>G Yu</strong>, 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. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p>
23 23 
 </div>
24 24 
 <div id="featured-articles" class="section level2">
site_src/content/tweets/index.html
History View file @ 7f332d20
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@@ -8,4 +8,4 @@ weight: 50
8 8
9 9 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
10 10 
 <p><font size="4"><strong>Leave me a message on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a></strong></font></p>
11 
-<p>{{% tweet 883301626022375424 %}}{{% tweet 883246854695256064 %}}{{% tweet 877576023109390336 %}}{{% tweet 875594411584782337 %}}{{% tweet 871775262152810496 %}}{{% tweet 867408666852511744 %}}{{% tweet 857665638600507393 %}}{{% tweet 840181267542994944 %}}{{% tweet 839831849736232962 %}}{{% tweet 830023569887391744 %}}{{% tweet 829398997735313408 %}}{{% tweet 824264788456984576 %}}{{% tweet 822383911258890242 %}}{{% tweet 811666431452450816 %}}{{% tweet 811661275889549312 %}}{{% tweet 797041236867686400 %}}{{% tweet 797037016403820546 %}}{{% tweet 794278716859879424 %}}{{% tweet 831952966701678592 %}}{{% tweet 788751417746059264 %}}{{% tweet 693123105707986944 %}}{{% tweet 691762302492790788 %}}{{% tweet 687933344219312128 %}}{{% tweet 684411780412526592 %}}{{% tweet 665188011047563268 %}}{{% tweet 664040586001915904 %}}{{% tweet 639507420054749184 %}}{{% tweet 671673570259509248 %}}{{% tweet 667490462693912576 %}}{{% tweet 660278158663401473 %}}{{% tweet 641251456595685376 %}}{{% tweet 559734740488818688 %}}{{% tweet 559762891478667264 %}}{{% tweet 561514846291001344 %}}{{% tweet 559542705663905793 %}}{{% tweet 561056244782227456 %}}{{% tweet 664085841766195200 %}}{{% tweet 664431087683260416 %}}{{% tweet 667706456045694976 %}}{{% tweet 663937183791759360 %}}{{% tweet 663771499589861376 %}}{{% tweet 667433534756397057 %}}{{% tweet 640573716733169664 %}}{{% tweet 664407764001779712 %}}{{% tweet 630500659960254464 %}}{{% tweet 547497335412899840 %}}{{% tweet 610364467939913728 %}}</p>
11 
+<p>{{% tweet 891144389715783680 %}}{{% tweet 883301626022375424 %}}{{% tweet 883246854695256064 %}}{{% tweet 877576023109390336 %}}{{% tweet 875594411584782337 %}}{{% tweet 871775262152810496 %}}{{% tweet 867408666852511744 %}}{{% tweet 857665638600507393 %}}{{% tweet 840181267542994944 %}}{{% tweet 839831849736232962 %}}{{% tweet 830023569887391744 %}}{{% tweet 829398997735313408 %}}{{% tweet 824264788456984576 %}}{{% tweet 822383911258890242 %}}{{% tweet 811666431452450816 %}}{{% tweet 811661275889549312 %}}{{% tweet 797041236867686400 %}}{{% tweet 797037016403820546 %}}{{% tweet 794278716859879424 %}}{{% tweet 831952966701678592 %}}{{% tweet 788751417746059264 %}}{{% tweet 693123105707986944 %}}{{% tweet 691762302492790788 %}}{{% tweet 687933344219312128 %}}{{% tweet 684411780412526592 %}}{{% tweet 665188011047563268 %}}{{% tweet 664040586001915904 %}}{{% tweet 639507420054749184 %}}{{% tweet 671673570259509248 %}}{{% tweet 667490462693912576 %}}{{% tweet 660278158663401473 %}}{{% tweet 641251456595685376 %}}{{% tweet 559734740488818688 %}}{{% tweet 559762891478667264 %}}{{% tweet 561514846291001344 %}}{{% tweet 559542705663905793 %}}{{% tweet 561056244782227456 %}}{{% tweet 664085841766195200 %}}{{% tweet 664431087683260416 %}}{{% tweet 667706456045694976 %}}{{% tweet 663937183791759360 %}}{{% tweet 663771499589861376 %}}{{% tweet 667433534756397057 %}}{{% tweet 640573716733169664 %}}{{% tweet 664407764001779712 %}}{{% tweet 630500659960254464 %}}{{% tweet 547497335412899840 %}}{{% tweet 610364467939913728 %}}</p>
site_src/content/tweets/index.rmd
History View file @ 7f332d20
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@@ -11,6 +11,7 @@ weight: 50
11 11
12 12
13 13 
 ````{r echo=FALSE}
14 
+blogdown::shortcode('tweet', '891144389715783680')
14 15 
 blogdown::shortcode('tweet', '883301626022375424')
15 16 
 blogdown::shortcode('tweet', '883246854695256064')
16 17 
 blogdown::shortcode('tweet', '877576023109390336')