git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106654 bc3139a8-67e5-0310-9ffc-ced21a209358
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Package: ggtree |
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Type: Package |
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Title: a phylogenetic tree viewer for different types of tree annotations |
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-Version: 1.1.9 |
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+Version: 1.1.10 |
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Author: Guangchuang Yu and Tommy Tsan-Yuk Lam |
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Maintainer: Guangchuang Yu <guangchuangyu@gmail.com> |
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Description: ggtree extends the ggplot2 plotting system which implemented the |
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+CHANGES IN VERSION 1.1.10 |
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+------------------------ |
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+ o solve overlapping branches for layout = "fan" || "radial", |
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+ that are coord_polar-ized layouts. |
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+ see https://github.com/GuangchuangYu/ggtree/issues/6, |
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+ contributed by Vincent Bonhomme. <2015-07-22, Wed> |
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+ |
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CHANGES IN VERSION 1.1.9 |
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------------------------ |
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o update add_legend to align legend text <2015-07-06, Mon> |
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@@ -17,6 +17,7 @@ |
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##' @importFrom ggplot2 ylab |
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##' @importFrom ggplot2 annotate |
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##' @importFrom ggplot2 scale_x_reverse |
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+##' @importFrom ggplot2 scale_y_continuous |
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##' @importFrom ggplot2 coord_flip |
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##' @importFrom ggplot2 coord_polar |
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##' @export |
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@@ -59,6 +60,8 @@ ggtree <- function(tr, |
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p <- p + scale_x_reverse() + coord_flip() |
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} else if (type == "fan" || type == "radial") { |
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p <- p + coord_polar(theta = "y") |
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+ ## refer to: https://github.com/GuangchuangYu/ggtree/issues/6 |
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+ p <- p + scale_y_continuous(limits=c(0, max(p$data$y))) |
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} |
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if (showDistance == FALSE) { |
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@@ -97,13 +100,13 @@ geom_tree <- function(layout="phylogram", color="black", linetype="solid", size= |
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lineend = "round" |
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if (layout == "phylogram" || layout == "fan") { |
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if (length(color) != 1) { |
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- color <- c(color, color) |
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+ color <- rep(color, 2) ## c(color, color) |
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} |
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if (length(linetype) != 1) { |
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- linetype <- c(linetype, linetype) |
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+ linetype <- rep(linetype, 2) ## c(linetype, linetype) |
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} |
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if (length(size) != 1) { |
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- size <- c(size, size) |
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+ size <- rep(size, 2) ## c(size, size) |
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} |
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geom_segment(aes(x = c(x[parent], x[parent]), |
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xend = c(x, x[parent]), |