Commit information:
Commit id: 56b987ad918722a45f128d44c0da1bbeb3b86419
fixed typo
Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-02-10 10:34:50 +0800
Author date: 2015-02-10 10:34:50 +0800
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@99299 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -1,7 +1,7 @@ |
1 | 1 |
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: 0.99.15 |
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+Version: 0.99.16 |
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Author: Guangchuang Yu |
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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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@@ -117,7 +117,7 @@ tree2d <- read.beast(system.file("extdata", "twoD.tree", package="ggtree")) |
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ggtree(tree2d, layout="cladogram", yscale="NLGS") |
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``` |
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|
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-In this example, y is scale by the number of N-glycosylation sites. This figure demonstrates the number of N-glycosylation sites increase along the trunk. User can highlight the trunk with different line size or color. |
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+In this example, y is scale by the number of N-glycosylation sites. This figure demonstrates the quantity of y increase along the trunk. User can highlight the trunk with different line size or color using the functions we described below. |
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## support multiple phylogenetic classes |
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@@ -125,7 +125,7 @@ In this example, y is scale by the number of N-glycosylation sites. This figure |
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`r Githubpkg("GuangchuangYu/ggtree")` defined several S4 classes to store phylogenetic object and its associated annotation, including: |
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|
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+ `jplace` |
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-+ `palm_rst` |
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++ `paml_rst` |
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+ `codeml_mlc` |
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+ `codeml` |
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+ `hyphy` |
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@@ -221,7 +221,7 @@ In `r Githubpkg("GuangchuangYu/ggtree")`, we implemented several functions to pa |
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Classes include: |
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-+ _`palm_rst`_ for _`rst`_ file obtained by [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html)[@yang_paml_2007], including _`BASEML`_ and _`CODEML`_. |
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++ _`paml_rst`_ for _`rst`_ file obtained by [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html)[@yang_paml_2007], including _`BASEML`_ and _`CODEML`_. |
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+ _`codeml_mlc`_ for _`mlc`_ file obtained by _`CODEML`_. |
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+ _`codeml`_ for interpreting _`rst`_ and _`mlc`_ files obtained by _`CODEML`_. |
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+ _`hyphy`_ for [HYPHY](http://hyphy.org/w/index.php/Main_Page)[@pond_hyphy_2005] output. |