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@@ -1,3 +1,33 @@
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1
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+CHANGES IN VERSION 1.1.20
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2
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+------------------------
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3
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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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4
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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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5
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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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6
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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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13
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+ o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
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14
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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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15
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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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19
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+ + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
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20
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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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23
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+CHANGES IN VERSION 1.1.19
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24
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+------------------------
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25
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+ o use fortify instead of fortify.phylo in fortify.multiPhylo,
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26
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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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27
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+ o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
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28
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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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29
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+ + these two packages is not commonly used, and will be loaded automatically when needed.
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30
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+
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1
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31
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CHANGES IN VERSION 1.1.18
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32
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------------------------
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3
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33
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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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@@ -112,7 +142,7 @@ CHANGES IN VERSION 1.1.2
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142
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o add examples folder in inst that contains sample data <2015-04-29, Wed>
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113
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143
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o update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
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114
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144
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o add line break if substitution longer than 50 character <2015-04-28, Tue>
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115
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- o upport calculating branch for time scale tree <2015-04-28, Tue>
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145
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+ o support calculating branch for time scale tree <2015-04-28, Tue>
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116
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146
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o remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
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117
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147
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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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118
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148
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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>
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