1. ggtree
  2. Commit 00bbb109fc35ad9cef505037ddf56350dfc18a3c
Browse code

bug fixed of rm.singleton.newick

guangchuang yu authored on 01/12/2016 04:40:01
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NEWS
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@@ -1,5 +1,6 @@
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 CHANGES IN VERSION 1.7.4
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 ------------------------
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+ o bug fixed of rm.singleton.newick, remove singleton parent instead of singleton <2016-12-01, Thu>
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  o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
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  o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
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    + https://github.com/GuangchuangYu/ggtree/issues/98
R/method-fortify.R
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@@ -87,9 +87,8 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {
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         p.singleton %<>% names %>% as.numeric
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         edge <- tree$edge
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         idx <- which(edge[,1] == p.singleton)
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-        singleton <- edge[idx, 2]
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-        sidx <- which(edge[,1] == singleton)
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-        edge[sidx,1] <- p.singleton
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+        sidx <- which(edge[,2] == p.singleton)
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+        edge[sidx,2] <- edge[idx, 2]
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         edge <- edge[-idx,]
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         tree$edge <- edge
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         tree$edge.length[sidx] %<>% add(., tree$edge.length[idx])
README.md
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@@ -4,7 +4,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 [![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" />
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