git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@116634 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: 1.3.15 |
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+Version: 1.3.16 |
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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 1.3.16 |
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+------------------------ |
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+ o update fortify.phylo to work with phylo that has missing value of edge length <2016-04-21, Thu> |
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+ + https://github.com/GuangchuangYu/ggtree/issues/54 |
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+ |
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CHANGES IN VERSION 1.3.15 |
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------------------------ |
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o geom_tiplab2 supports parameter hjust <2016-04-18, Mon> |
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@@ -460,6 +460,13 @@ fortify.phylo <- function(model, data, layout="rectangular", |
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} else { |
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tree <- model |
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} |
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+ |
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+ if (! is.null(tree$edge.length)) { |
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+ if (any(is.na(tree$edge.length))) { |
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+ warning("'edge.length' contains NA values...\n## setting 'edge.length' to NULL automatically when plotting the tree...") |
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+ tree$edge.length <- NULL |
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+ } |
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+ } |
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df <- as.data.frame(tree, layout=layout, ...) |
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idx <- is.na(df$parent) |
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@@ -525,6 +532,7 @@ as.data.frame.phylo_ <- function(x, layout="rectangular", |
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edge <- as.data.frame(x[["edge"]]) |
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colnames(edge) <- c("parent", "node") |
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+ |
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if (! is.null(x$edge.length)) { |
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edge$length <- x$edge.length |
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if (branch.length == "none") { |