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git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109354 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 08/10/2015 10:09:17
Showing 1 changed files

  • NEWS index aa86cd8..55d8734 100644
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+CHANGES IN VERSION 1.1.20
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+------------------------
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+ o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
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+ o bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>
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+ o bug fixed of subview for considering aes mapping of x and y <2015-09-03, Thu>
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+ o update vignette by adding r8s example <2015-09-02, Wed>
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+ o defined r8s class, see http://loco.biosci.arizona.edu/r8s/  <2015-09-02, Wed>
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+   + add r8s sample files
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+   + read.r8s, parser function
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+   + fortify method
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+   + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
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+ o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>   
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+ o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
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+ o add mrsd parameter for user to specify 'most recent sampling date' for time tree <2015-09-01, Tue>
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+   - remove 'time_scale' parameter.
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+ o defined 'raxml' class for RAxML bootstrapping analysis result <2015-09-01, Tue>
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+   + see http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html
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+   + read.raxml, parser function
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+   + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
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+   + fortify.raxml method
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+ o bug fixed in edgeNum2nodeNum for jplace parsing jplace file <2015-09-01, Tue>
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+ 
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+CHANGES IN VERSION 1.1.19
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+------------------------
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+ o use fortify instead of fortify.phylo in fortify.multiPhylo, 
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+   so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon>
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+ o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
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+ o remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon>
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+   + these two packages is not commonly used, and will be loaded automatically when needed.
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+ 
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 CHANGES IN VERSION 1.1.18
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  o layout name change to 'rectangular', 'slanted', 'circular'/'fan' for phylogram and cladogram (if branch.length = 'none')
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  o add examples folder in inst that contains sample data <2015-04-29, Wed>
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  o update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
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  o add line break if substitution longer than 50 character <2015-04-28, Tue>
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- o upport calculating branch for time scale tree <2015-04-28, Tue>
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+ o support calculating branch for time scale tree <2015-04-28, Tue>
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  o remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
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  o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>
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  o scale_color accepts user specific interval and output contains 'scale' attribute that can be used for adding legend <2015-04-28, Tue>