1. ggtree
  2. NEWS
Browse code

update msaplot to use DNAbin/AAbin

guangchuang yu authored on 14/12/2017 10:29:44
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1 1 
 CHANGES IN VERSION 1.11.3
2 2 
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3 
+ o update msaplot to use DNAbin/AAbin internally and also compatible with treedata object <2017-12-14, Thu>
3 4 
  o clean up code <2017-12-13, Thu>
4 5 
  o remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3) <2017-12-07, Thu>
5 6
Browse code

clean up code

guangchuang yu authored on 14/12/2017 08:47:21
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1 1 
 CHANGES IN VERSION 1.11.3
2 2 
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3 
+ o clean up code <2017-12-13, Thu>
3 4 
  o remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3) <2017-12-07, Thu>
4 5
5 6 
 CHANGES IN VERSION 1.11.2
Browse code

remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3)

guangchuang yu authored on 07/12/2017 07:21:58
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+CHANGES IN VERSION 1.11.3
2 
+------------------------
3 
+ o remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3) <2017-12-07, Thu>
4 
+
1 5 
 CHANGES IN VERSION 1.11.2
2 6 
 ------------------------
3 7 
  o keep tree order (previously using postorder) <2017-12-06-Wed>
Browse code

keep tree order #157

guangchuang yu authored on 06/12/2017 02:01:19
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1 1 
 CHANGES IN VERSION 1.11.2
2 2 
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3 
+ o keep tree order (previously using postorder) <2017-12-06-Wed>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/157
3 5 
  o remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>
4 6 
  o deprecate subview, annotation_image and phylopic; remove theme_transparent <2017-12-04, Mon>
5 7 
  o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>
Browse code

remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>

guangchuang yu authored on 05/12/2017 11:05:11
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1 1 
 CHANGES IN VERSION 1.11.2
2 2 
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3 
+ o remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>
3 4 
  o deprecate subview, annotation_image and phylopic; remove theme_transparent <2017-12-04, Mon>
4 5 
  o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>
5 6 
  o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>
Browse code

remove theme_transparent

guangchuang yu authored on 04/12/2017 12:41:52
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1 1 
 CHANGES IN VERSION 1.11.2
2 2 
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3 
- o deprecate subview, annotation_image and phylopic <2017-12-04, Mon>
3 
+ o deprecate subview, annotation_image and phylopic; remove theme_transparent <2017-12-04, Mon>
4 4 
  o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>
5 5 
  o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>
6 6
Browse code

ggtree with image files

guangchuang yu authored on 04/12/2017 11:45:07
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+CHANGES IN VERSION 1.11.2
2 
+------------------------
3 
+ o deprecate subview, annotation_image and phylopic <2017-12-04, Mon>
4 
+ o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>
5 
+ o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>
6 
+
1 7 
 CHANGES IN VERSION 1.11.1
2 8 
 ------------------------
3 9 
  o bug fixed in geom_tiplab, now `offset` parameter works with `align=TRUE`. <2017-11-20, Mon>
Browse code

geom_tiplab enhancement

guangchuang yu authored on 20/11/2017 13:20:02
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 CHANGES IN VERSION 1.11.1
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+ o bug fixed in geom_tiplab, now `offset` parameter works with `align=TRUE`. <2017-11-20, Mon>
3 4 
  o enable mrsd parameter for treedata object <2017-11-15, Wed>
4 5 
  o set_hilight_legend supports alpha parameter <2017-11-15, Wed>
5 6 
    + https://github.com/GuangchuangYu/ggtree/issues/149
Browse code

mrsd for treedata object

guangchuang yu authored on 15/11/2017 07:45:39
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+CHANGES IN VERSION 1.11.1
2 
+------------------------
3 
+ o enable mrsd parameter for treedata object <2017-11-15, Wed>
4 
+ o set_hilight_legend supports alpha parameter <2017-11-15, Wed>
5 
+   + https://github.com/GuangchuangYu/ggtree/issues/149
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+
1 7 
 CHANGES IN VERSION 1.9.4
2 8 
 ------------------------
3 9 
  o geom_hilight_encircle and geom_cladelabel2 <2017-09-12, Tue>
Browse code

fixed R check for #152

guangchuang yu authored on 12/09/2017 10:01:00
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 CHANGES IN VERSION 1.9.4
2 2 
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+ o geom_hilight_encircle and geom_cladelabel2 <2017-09-12, Tue>
4 
+   + https://github.com/GuangchuangYu/ggtree/pull/152
3 5 
  o set_hilight_legend <2017-08-30, Wed>
4 6 
  o geom_motif for aligned motif <2017-08-22, Tue>
5 7 
    + https://github.com/GuangchuangYu/ggtree/issues/148
Browse code

set_hilight_legend

guangchuang yu authored on 30/08/2017 06:34:31
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 CHANGES IN VERSION 1.9.4
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+ o set_hilight_legend <2017-08-30, Wed>
3 4 
  o geom_motif for aligned motif <2017-08-22, Tue>
4 5 
    + https://github.com/GuangchuangYu/ggtree/issues/148
5 6 
  o fixed `R CMD build` error: cannot stat 'ggtree/site_src/themes': No such file or directory <2017-08-22, Tue>
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
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+ o geom_motif for aligned motif <2017-08-22, Tue>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/148
3 5 
  o fixed `R CMD build` error: cannot stat 'ggtree/site_src/themes': No such file or directory <2017-08-22, Tue>
4 6
5 7 
 CHANGES IN VERSION 1.9.3
Browse code

update docs

guangchuang yu authored on 22/08/2017 06:08:09
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+CHANGES IN VERSION 1.9.4
2 
+------------------------
3 
+ o fixed `R CMD build` error: cannot stat 'ggtree/site_src/themes': No such file or directory <2017-08-22, Tue>
4 
+
1 5 
 CHANGES IN VERSION 1.9.3
2 6 
 ------------------------
3 7 
  o update to using !! in tidyr::gather for compatible with tidyr 0.7.0 <2017-08-03, Thu>
Browse code

compatible with tidyr 0.7.0

guangchuang yu authored on 03/08/2017 05:05:40
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1 1 
 CHANGES IN VERSION 1.9.3
2 2 
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+ o update to using !! in tidyr::gather for compatible with tidyr 0.7.0 <2017-08-03, Thu>
3 4 
  o now geom_text2, geom_label2, geom_point2 and geom_segment2 work with ggplot2 <2017-08-01, Tue>
4 5 
  o update fortify.jplace to support number of placement (nplace) <2017-07-27, Thu>
5 6
Browse code

now geom_text2, geom_label2, geom_point2 and geom_segment2 work with ggplot2

guangchuang yu authored on 01/08/2017 12:22:46
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1 1 
 CHANGES IN VERSION 1.9.3
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+ o now geom_text2, geom_label2, geom_point2 and geom_segment2 work with ggplot2 <2017-08-01, Tue>
3 4 
  o update fortify.jplace to support number of placement (nplace) <2017-07-27, Thu>
4 5
5 6 
 CHANGES IN VERSION 1.9.2
Browse code

jplace

guangchuang yu authored on 27/07/2017 03:46:36
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+CHANGES IN VERSION 1.9.3
2 
+------------------------
3 
+ o update fortify.jplace to support number of placement (nplace) <2017-07-27, Thu>
4 
+
1 5 
 CHANGES IN VERSION 1.9.2
2 6 
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3 7 
  o add bg_line and height parameter in msaplot <2017-07-26, Wed>
Browse code

update msaplot

guangchuang yu authored on 26/07/2017 07:46:20
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 CHANGES IN VERSION 1.9.2
2 2 
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3 
+ o add bg_line and height parameter in msaplot <2017-07-26, Wed>
4 
+   + use can set bg_line = FALSE and height = 1 to plot more beautiful alignment
3 5 
  o extend parameter in geom_cladebar <2017-07-26, Wed>
4 6 
    + https://github.com/GuangchuangYu/ggtree/issues/142#issuecomment-317817995
5 7 
  o scaleClade works after calling viewClade <2017-07-20, Thu>
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
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1 1 
 CHANGES IN VERSION 1.9.2
2 2 
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+ o extend parameter in geom_cladebar <2017-07-26, Wed>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/142#issuecomment-317817995
3 5 
  o scaleClade works after calling viewClade <2017-07-20, Thu>
4 6 
    + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/QVSryszPaFY
5 7 
  o gheatmap support handling collapsed tree <2017-06-29, Thu>
Browse code

scaleClade works after calling viewClade

guangchuang yu authored on 20/07/2017 07:44:44
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1 1 
 CHANGES IN VERSION 1.9.2
2 2 
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+ o scaleClade works after calling viewClade <2017-07-20, Thu>
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+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/QVSryszPaFY
3 5 
  o gheatmap support handling collapsed tree <2017-06-29, Thu>
4 6 
    + https://github.com/GuangchuangYu/ggtree/issues/137
5 7
Browse code

gheatmap supports collapsed tree

guangchuang yu authored on 29/06/2017 05:10:11
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+CHANGES IN VERSION 1.9.2
2 
+------------------------
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+ o gheatmap support handling collapsed tree <2017-06-29, Thu>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/137
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+
1 6 
 CHANGES IN VERSION 1.9.1
2 7 
 ------------------------
3 8 
  o now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon>
Browse code

now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon>

guangchuang yu authored on 19/06/2017 13:28:29
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 CHANGES IN VERSION 1.9.1
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+ o now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon>
3 4 
  o geom_cladelabel support `angle="auto"` for circular layout tree <2017-05-05, Fri>
4 5
5 6 
 CHANGES IN VERSION 1.8.0
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geom_cladelabel now support `angle="auto"`

GuangchuangYu authored on 05/05/2017 21:01:50
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+CHANGES IN VERSION 1.9.1
2 
+------------------------
3 
+ o geom_cladelabel support `angle="auto"` for circular layout tree <2017-05-05, Fri>
4 
+
1 5 
 CHANGES IN VERSION 1.8.0
2 6 
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3 7 
  o BioC 3.5 release <2017-04-26, Wed>
Browse code

bioc-3.6

guangchuang yu authored on 27/04/2017 07:25:59
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+CHANGES IN VERSION 1.8.0
2 
+------------------------
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+ o BioC 3.5 release <2017-04-26, Wed>
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+
1 5 
 CHANGES IN VERSION 1.7.11
2 6 
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3 7 
  o remove layout.method parameter <2017-04-20, Thu>
Browse code

remove layout.method

guangchuang yu authored on 20/04/2017 02:28:57
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+CHANGES IN VERSION 1.7.11
2 
+------------------------
3 
+ o remove layout.method parameter <2017-04-20, Thu>
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+   + https://github.com/GuangchuangYu/ggtree/issues/118#issuecomment-295130818
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+   + https://github.com/GuangchuangYu/ggtree/issues/125
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+
1 7 
 CHANGES IN VERSION 1.7.10
2 8 
 ------------------------
3 9 
  o add message for subview, inset, phylopic, theme_transparent and theme_inset <2017-03-23, Thu>
Browse code

message for defunct functions

guangchuang yu authored on 23/03/2017 03:40:26
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+ o add message for subview, inset, phylopic, theme_transparent and theme_inset <2017-03-23, Thu>
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+   + will be defunct in version >= 1.9.0
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+   + user should use ggimage package to annotate tree with graphic object or image file
3 6 
  o update subview to support mainview produced by `ggplot() + layers` <2017-03-13, Mon>
4 7
5 8 
 CHANGES IN VERSION 1.7.9
Browse code

update subview

guangchuang yu authored on 13/03/2017 05:39:11
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+CHANGES IN VERSION 1.7.10
2 
+------------------------
3 
+ o update subview to support mainview produced by `ggplot() + layers` <2017-03-13, Mon>
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+
1 5 
 CHANGES IN VERSION 1.7.9
2 6 
 ------------------------
3 7 
  o fixed geom_range to support height_0.95_HPD <2017-03-03, Fri>
Browse code

fixed geom_range to support height_0.95_HPD <2017-03-03, Fri>

guangchuang yu authored on 03/03/2017 05:42:32
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 CHANGES IN VERSION 1.7.9
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+ o fixed geom_range to support height_0.95_HPD <2017-03-03, Fri>
3 4 
  o fixed geom_tiplab(geom='label') <2017-03-02, Thu>
4 5 
    + https://github.com/GuangchuangYu/ggtree/issues/115
5 6
Browse code

fixed #115

guangchuang yu authored on 02/03/2017 02:49:53
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+CHANGES IN VERSION 1.7.9
2 
+------------------------
3 
+ o fixed geom_tiplab(geom='label') <2017-03-02, Thu>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/115
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+
1 6 
 CHANGES IN VERSION 1.7.8
2 7 
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3 8 
  o get_taxa_name now sorted by taxa position and also support whole tree <2017-03-01, Wed>
Browse code

o unrooted layout support branch.length="none", fixed #114

guangchuang yu authored on 01/03/2017 08:49:58
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 CHANGES IN VERSION 1.7.8
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+ o get_taxa_name now sorted by taxa position and also support whole tree <2017-03-01, Wed>
4 
+ o unrooted layout support branch.length="none", fixed #114 <2017-03-01, Wed>
3 5 
  o remove apeBootstrap and raxml object support as they were removed from treeio <2017-02-28, Tue>
4 6
5 7 
 CHANGES IN VERSION 1.7.7
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remove apeBootstrap and raxml object support as they were removed from treeio

guangchuang yu authored on 28/02/2017 07:11:57
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+CHANGES IN VERSION 1.7.8
2 
+------------------------
3 
+ o remove apeBootstrap and raxml object support as they were removed from treeio <2017-02-28, Tue>
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+
1 5 
 CHANGES IN VERSION 1.7.7
2 6 
 ------------------------
3 7 
  o supports parse="emoji" in geom_cladelabel, geom_text2, geom_label2, geom_tiplab, geom_tiplab2 <2017-02-16, Thu>
Browse code

parse="emoji" :)

guangchuang yu authored on 16/02/2017 06:54:38
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 CHANGES IN VERSION 1.7.7
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- o geom_cladelabel support parse="emoji" <2017-02-16, Thu>
3 
+ o supports parse="emoji" in geom_cladelabel, geom_text2, geom_label2, geom_tiplab, geom_tiplab2 <2017-02-16, Thu>
4 4 
  o aes(subset) now support logical vector contains NA <2017-02-16, Thu>
5 5 
  o add legend transparency to theme_transparent <2017-02-13, Mon>
6 6 
    + <https://github.com/GuangchuangYu/ggtree/pull/112>
Browse code

subset supports logical vector contains NA, and geom_cladelabel supports parsing emoji

guangchuang yu authored on 16/02/2017 06:10:17
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1 1 
 CHANGES IN VERSION 1.7.7
2 2 
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3 
+ o geom_cladelabel support parse="emoji" <2017-02-16, Thu>
4 
+ o aes(subset) now support logical vector contains NA <2017-02-16, Thu>
3 5 
  o add legend transparency to theme_transparent <2017-02-13, Mon>
4 6 
    + <https://github.com/GuangchuangYu/ggtree/pull/112>
5 7 
  o update citation info <2017-01-20, Fri>
6 
-
8 
+
7 9 
 CHANGES IN VERSION 1.7.6
8 10 
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9 11 
  o inset support reverse scale <2017-01-05, Thu>
Browse code

update docs

guangchuang yu authored on 13/02/2017 05:33:14
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 CHANGES IN VERSION 1.7.7
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+ o add legend transparency to theme_transparent <2017-02-13, Mon>
4 
+   + <https://github.com/GuangchuangYu/ggtree/pull/112>
3 5 
  o update citation info <2017-01-20, Fri>
4 6
5 7 
 CHANGES IN VERSION 1.7.6
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update citation

GuangchuangYu authored on 20/01/2017 05:21:52
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+CHANGES IN VERSION 1.7.7
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+------------------------
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+ o update citation info <2017-01-20, Fri>
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+
1 5 
 CHANGES IN VERSION 1.7.6
2 6 
 ------------------------
3 7 
  o inset support reverse scale <2017-01-05, Thu>
Browse code

reverse_x and reverse_y parameters for inset

guangchuang yu authored on 05/01/2017 03:23:11
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+CHANGES IN VERSION 1.7.6
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+------------------------
3 
+ o inset support reverse scale <2017-01-05, Thu>
4 
+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/_JPfm71Z8nM/6gL93oxHFQAJ
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+
1 6 
 CHANGES IN VERSION 1.7.5
2 7 
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3 8 
  o disable labeling collapsed node as tip <2017-01-03, Tue>
Browse code

not labeling collapsed clade as tip

guangchuang yu authored on 03/01/2017 03:47:16
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 CHANGES IN VERSION 1.7.5
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+ o disable labeling collapsed node as tip <2017-01-03, Tue>
4 
+   + https://groups.google.com/forum/#!topic/bioc-ggtree/nReqJatMvJQ
3 5 
  o fortify.phylo4d via converting phylo4d to treedata object <2016-12-28, Wed>
4 6 
  o improve viewClade function, use coord_cartesian instead of xlim <2016-12-28, Wed>
5 7 
  o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
Browse code

fortify.phylo4d via converting phylo4d to treedata object

guangchuang yu authored on 28/12/2016 13:49:47
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 CHANGES IN VERSION 1.7.5
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+ o fortify.phylo4d via converting phylo4d to treedata object <2016-12-28, Wed>
3 4 
  o improve viewClade function, use coord_cartesian instead of xlim <2016-12-28, Wed>
4 5 
  o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
5 6
Browse code

better viewClade

guangchuang yu authored on 28/12/2016 08:08:07
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1 1 
 CHANGES IN VERSION 1.7.5
2 2 
 ------------------------
3 
+ o improve viewClade function, use coord_cartesian instead of xlim <2016-12-28, Wed>
3 4 
  o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
4 
-
5 
+
5 6 
 CHANGES IN VERSION 1.7.4
6 7 
 ------------------------
7 8 
  o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue>
Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
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1 
+CHANGES IN VERSION 1.7.5
2 
+------------------------
3 
+ o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
4 
+
1 5 
 CHANGES IN VERSION 1.7.4
2 6 
 ------------------------
3 7 
  o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue>
Browse code

is.ggtree

guangchuang yu authored on 06/12/2016 07:53:23
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1 1 
 CHANGES IN VERSION 1.7.4
2 2 
 ------------------------
3 
+ o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue>
3 4 
  o now branch.length can set to feature available in phylo4d@data and yscale is supported for phylo4d object <2016-12-06, Tue>
4 5 
  o bug fixed of rm.singleton.newick, remove singleton parent instead of singleton <2016-12-01, Thu>
5 6 
  o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
Browse code

branch.length support phylo4d@data

guangchuang yu authored on 06/12/2016 05:42:11
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1 1 
 CHANGES IN VERSION 1.7.4
2 2 
 ------------------------
3 
+ o now branch.length can set to feature available in phylo4d@data and yscale is supported for phylo4d object <2016-12-06, Tue>
3 4 
  o bug fixed of rm.singleton.newick, remove singleton parent instead of singleton <2016-12-01, Thu>
4 5 
  o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
5 6 
  o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
Browse code

bug fixed of rm.singleton.newick

guangchuang yu authored on 01/12/2016 04:40:01
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1 1 
 CHANGES IN VERSION 1.7.4
2 2 
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3 
+ o bug fixed of rm.singleton.newick, remove singleton parent instead of singleton <2016-12-01, Thu>
3 4 
  o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
4 5 
  o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
5 6 
    + https://github.com/GuangchuangYu/ggtree/issues/98
Browse code

postorder

guangchuang yu authored on 28/11/2016 05:42:43
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1 1 
 CHANGES IN VERSION 1.7.4
2 2 
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3 
+ o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
3 4 
  o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
4 5 
    + https://github.com/GuangchuangYu/ggtree/issues/98
5 6 
  o groupOTU method now accept 'overlap = c("overwrite", "origin", "abandon")' parameter <2016-11-16, Wed>
Browse code

phylo4d

guangchuang yu authored on 24/11/2016 05:04:08
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1 1 
 CHANGES IN VERSION 1.7.4
2 2 
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3 
+ o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/98
3 5 
  o groupOTU method now accept 'overlap = c("overwrite", "origin", "abandon")' parameter <2016-11-16, Wed>
4 6 
    + https://groups.google.com/forum/#!topic/bioc-ggtree/Q4LnwoTf1DM
5 7
Browse code

overlap parameter in groupOTU

guangchuang yu authored on 16/11/2016 05:54:24
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History View file @3846507e
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1 
+CHANGES IN VERSION 1.7.4
2 
+------------------------
3 
+ o groupOTU method now accept 'overlap = c("overwrite", "origin", "abandon")' parameter <2016-11-16, Wed>
4 
+   + https://groups.google.com/forum/#!topic/bioc-ggtree/Q4LnwoTf1DM
5 
+
1 6 
 CHANGES IN VERSION 1.7.3
2 7 
 ------------------------
3 8 
  o drop.tip method for NHX object <2016-11-11, Fri>
Browse code

fixed drop.tip issues

guangchuang yu authored on 11/11/2016 05:33:47
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1 1 
 CHANGES IN VERSION 1.7.3
2 2 
 ------------------------
3 
+ o drop.tip method for NHX object <2016-11-11, Fri>
3 4 
  o update startup message <2016-11-09, Wed>
4 5 
  o reverse timescale x-axis <2016-11-07, Mon>
5 6 
    + https://github.com/GuangchuangYu/ggtree/issues/87
Browse code

update news

guangchuang yu authored on 09/11/2016 08:00:46
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1 1 
 CHANGES IN VERSION 1.7.3
2 2 
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3 
+ o update startup message <2016-11-09, Wed>
3 4 
  o reverse timescale x-axis <2016-11-07, Mon>
4 5 
    + https://github.com/GuangchuangYu/ggtree/issues/87
5 6
Browse code

revts

guangchuang yu authored on 07/11/2016 03:16:33
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1 
+CHANGES IN VERSION 1.7.3
2 
+------------------------
3 
+ o reverse timescale x-axis <2016-11-07, Mon>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/87
5 
+
1 6 
 CHANGES IN VERSION 1.7.2
2 7 
 ------------------------
3 8 
  o make missing colors in gheatmap invisible (previously use 'white') <2016-11-03, Thu>
Browse code

make missing color invisible

GuangchuangYu authored on 03/11/2016 15:30:13
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1 1 
 CHANGES IN VERSION 1.7.2
2 2 
 ------------------------
3 
+ o make missing colors in gheatmap invisible (previously use 'white') <2016-11-03, Thu>
3 4 
  o xlim_expand for setting x axis limits of specific panel <2016-11-01, Tue>
4 5 
    + xlim_tree is now a specific case of xlim_expand(xlim, panel='Tree')
5 6 
  o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
Browse code

xlim_expand

guangchuang yu authored on 01/11/2016 02:38:09
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1 1 
 CHANGES IN VERSION 1.7.2
2 2 
 ------------------------
3 
- o expand_xlim for setting x axis limits of specific panel <2016-11-01, Tue>
4 
-   + xlim_tree is now a specific case of expand_xlim(xlim, panel='Tree')
3 
+ o xlim_expand for setting x axis limits of specific panel <2016-11-01, Tue>
4 
+   + xlim_tree is now a specific case of xlim_expand(xlim, panel='Tree')
5 5 
  o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
6 6 
    + https://github.com/GuangchuangYu/ggtree/issues/84
7 7
Browse code

expand_xlim

guangchuang yu authored on 01/11/2016 02:23:02
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1 1 
 CHANGES IN VERSION 1.7.2
2 2 
 ------------------------
3 
+ o expand_xlim for setting x axis limits of specific panel <2016-11-01, Tue>
4 
+   + xlim_tree is now a specific case of expand_xlim(xlim, panel='Tree')
3 5 
  o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
4 6 
    + https://github.com/GuangchuangYu/ggtree/issues/84
5 7
6 8 
 CHANGES IN VERSION 1.7.1
7 9 
 ------------------------
8 10 
  o xlim_tree layer and test <2016-10-31, Mon>
9 
-   + set x axis limit for Tree panel for facet_plot
11 
+   + set x axis limits for Tree panel for facet_plot
10 12 
  o update read.nhx <2016-10-30, Sun>
11 13 
    + add tip numbers to @nhx_tags and add tests
12 14 
    + https://github.com/GuangchuangYu/ggtree/pull/83
Browse code

bug fixed of parsing treetext in beast file

guangchuang yu authored on 31/10/2016 11:29:54
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1 
+CHANGES IN VERSION 1.7.2
2 
+------------------------
3 
+ o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/84
5 
+
1 6 
 CHANGES IN VERSION 1.7.1
2 7 
 ------------------------
3 8 
  o xlim_tree layer and test <2016-10-31, Mon>
Browse code

xlim_tree

guangchuang yu authored on 31/10/2016 07:41:12
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1 1 
 CHANGES IN VERSION 1.7.1
2 2 
 ------------------------
3 
- o set_tree_xlim function and test <2016-10-31, Mon>
3 
+ o xlim_tree layer and test <2016-10-31, Mon>
4 4 
    + set x axis limit for Tree panel for facet_plot
5 5 
  o update read.nhx <2016-10-30, Sun>
6 6 
    + add tip numbers to @nhx_tags and add tests
Browse code

set_tree_xlim

guangchuang yu authored on 31/10/2016 04:10:22
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1 1 
 CHANGES IN VERSION 1.7.1
2 2 
 ------------------------
3 
+ o set_tree_xlim function and test <2016-10-31, Mon>
4 
+   + set x axis limit for Tree panel for facet_plot
5 
+ o update read.nhx <2016-10-30, Sun>
6 
+   + add tip numbers to @nhx_tags and add tests
7 
+   + https://github.com/GuangchuangYu/ggtree/pull/83
8 
+   + store nhx_tags$node as numeric values <2016-10-31, Mon>
3 9 
  o facet_plot supports ggbio::geom_alignment <2016-10-26, Wed>
4 10 
    + https://github.com/tengfei/ggbio/issues/83
5 11 
  o make tree stats available in facet_plot <2016-10-24, Mon>
Browse code

facet_plot supports ggbio::geom_alignment

guangchuang yu authored on 26/10/2016 08:27:56
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1 1 
 CHANGES IN VERSION 1.7.1
2 2 
 ------------------------
3 
+ o facet_plot supports ggbio::geom_alignment <2016-10-26, Wed>
4 
+   + https://github.com/tengfei/ggbio/issues/83
3 5 
  o make tree stats available in facet_plot <2016-10-24, Mon>
4 6
5 7 
 CHANGES IN VERSION 1.6.0
Browse code

make tree stats available in facet_plot <2016-10-24, Mon>

guangchuang yu authored on 24/10/2016 07:52:43
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1 
+CHANGES IN VERSION 1.7.1
2 
+------------------------
3 
+ o make tree stats available in facet_plot <2016-10-24, Mon>
4 
+
1 5 
 CHANGES IN VERSION 1.6.0
2 6 
 ------------------------
3 7 
  o BioC 3.4 released <2016-10-18, Tue>
4 
-
8 
+
5 9 
 CHANGES IN VERSION 1.5.17
6 10 
 ------------------------
7 11 
  o read.nhx support newick file <2016-10-17, Mon>
Browse code

bioc 3.5

guangchuang yu authored on 18/10/2016 01:23:55
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1 
+CHANGES IN VERSION 1.6.0
2 
+------------------------
3 
+ o BioC 3.4 released <2016-10-18, Tue>
4 
+
1 5 
 CHANGES IN VERSION 1.5.17
2 6 
 ------------------------
3 7 
  o read.nhx support newick file <2016-10-17, Mon>
Browse code

read.nhx supports newick file

guangchuang yu authored on 17/10/2016 03:02:31
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1 
+CHANGES IN VERSION 1.5.17
2 
+------------------------
3 
+ o read.nhx support newick file <2016-10-17, Mon>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/79
5 
+
1 6 
 CHANGES IN VERSION 1.5.16
2 7 
 ------------------------
3 8 
  o read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue>
Browse code

read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue>

guangchuang yu authored on 11/10/2016 10:02:10
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1 1 
 CHANGES IN VERSION 1.5.16
2 2 
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3 
+ o read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue>
4 
+   + https://www.biostars.org/p/210401/#216128
3 5 
  o fixed aes mapping in geom_strip <2016-10-11, Tue>
4 6 
  o fixed R check <2016-10-10, Mon>
5 7 
    + check.aes parameter is not available in release version of ggplot2 yet
Browse code

fixed aes mapping in geom_strip <2016-10-11, Tue>

guangchuang yu authored on 11/10/2016 06:41:22
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1 1 
 CHANGES IN VERSION 1.5.16
2 2 
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3 
+ o fixed aes mapping in geom_strip <2016-10-11, Tue>
3 4 
  o fixed R check <2016-10-10, Mon>
4 5 
    + check.aes parameter is not available in release version of ggplot2 yet
5 
-
6 
+
6 7 
 CHANGES IN VERSION 1.5.15
7 8 
 ------------------------
8 9 
  o check.aes for layers defined in ggtree <2016-10-07, Fri>
Browse code

fixed R check

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122173 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 11/10/2016 01:31:56
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1 
+CHANGES IN VERSION 1.5.16
2 
+------------------------
3 
+ o fixed R check <2016-10-10, Mon>
4 
+   + check.aes parameter is not available in release version of ggplot2 yet
5 
+
1 6 
 CHANGES IN VERSION 1.5.15
2 7 
 ------------------------
3 8 
  o check.aes for layers defined in ggtree <2016-10-07, Fri>
Browse code

version 1.5.15

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122021 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 07/10/2016 05:18:29
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1 
+CHANGES IN VERSION 1.5.15
2 
+------------------------
3 
+ o check.aes for layers defined in ggtree <2016-10-07, Fri>
4 
+ o recalculate 'angle' when collapse, expand and rotate clade <2016-10-06, Thu>
5 
+   + https://github.com/GuangchuangYu/ggtree/issues/78
6 
+
1 7 
 CHANGES IN VERSION 1.5.14
2 8 
 ------------------------
3 9 
  o subset tip in geom_tiplab2 <2016-10-05, Wed>
Browse code

subset tip in geom_tiplab2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@121788 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 05/10/2016 08:52:08
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1 1 
 CHANGES IN VERSION 1.5.14
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3 
+ o subset tip in geom_tiplab2 <2016-10-05, Wed>
3 4 
  o add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>
4 5 
    + https://github.com/hadley/ggplot2/issues/1797
5 6 
  o unit test for groupOTU and groupClade <2016-09-22, Thu>
Browse code

add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@121523 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 29/09/2016 05:55:59
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1 1 
 CHANGES IN VERSION 1.5.14
2 2 
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3 
+ o add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>
4 
+   + https://github.com/hadley/ggplot2/issues/1797
3 5 
  o unit test for groupOTU and groupClade <2016-09-22, Thu>
4 6 
  o groupOTU label groups by input group names (when input is a named list) <2016-09-22, Thu>
5 7 
  o update angle calculation for geom_tiplab <2016-09-13, Thu>
Browse code

unit test of groupOTU & groupClade

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@121230 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 22/09/2016 05:42:40
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1 1 
 CHANGES IN VERSION 1.5.14
2 2 
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3 
+ o unit test for groupOTU and groupClade <2016-09-22, Thu>
4 
+ o groupOTU label groups by input group names (when input is a named list) <2016-09-22, Thu>
3 5 
  o update angle calculation for geom_tiplab <2016-09-13, Thu>
4 6 
  o as.polytomy to collapse binary tree to polytomy by applying 'fun' to selected 'feature' (e.g. bootstrap value less than 70). <2016-09-13, Tue>
5 7 
    + currently only phylo object supported.
6 8 
    + add test for as.polytomy
7 
-
9 
+
8 10 
 CHANGES IN VERSION 1.5.13
9 11 
 ------------------------
10 12 
  o facet_plot for plotting data with tree <2016-09-06, Tue>
... ... 
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14 16 
    + colnames_offset_y
15 17 
    + hjust
16 18 
  o offset parameter in geom_tiplab and geom_tiplab2 <2016-09-05, Mon>
17 
-
19 
+
18 20 
 CHANGES IN VERSION 1.5.12
19 21 
 ------------------------
20 22 
  o use data in all layers instead of the base layer for coordination calculation in subview <2016-09-01, Thu>
21 23 
  o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
22 
-
24 
+
23 25 
 CHANGES IN VERSION 1.5.11
24 26 
 ------------------------
25 27 
  o gheatmap works with matrix <2016-08-28, Sun>
... ... 
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28 30 
  o bug fixed in geom_tiplab <2016-08-17, Wed>
29 31 
    + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
30 32 
  o update citation info, add doi. <2016-08-16, Tue>
31 
-
33 
+
32 34 
 CHANGES IN VERSION 1.5.10
33 35 
 ------------------------
34 36 
  o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
35 37 
    + https://github.com/GuangchuangYu/ggtree/issues/72
36 
-
38 
+
37 39 
 CHANGES IN VERSION 1.5.9
38 40 
 ------------------------
39 41 
  o update citation info <2016-08-12, Fri>
40 
-
42 
+
41 43 
 CHANGES IN VERSION 1.5.8
42 44 
 ------------------------
43 45 
  o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
44 46 
  o geom_cladelabel support parsing expression <2016-08-11, Thu>
45 
-
47 
+
46 48 
 CHANGES IN VERSION 1.5.7
47 49 
 ------------------------
48 50 
  o geom_strip can accept taxa name as input but labeling strip will not supported.
49 51 
    To support labeling strip, user need to input node id  <2016-07-27, Wed>
50 
- o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
51 
-
52 
+ o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
53 
+
52 54 
 CHANGES IN VERSION 1.5.6
53 55 
 ------------------------
54 56 
  o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
... ... 
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69 71 
  o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
70 72 
    + as.Date won't work for BCE time.
71 73 
    + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
72 
-
74 
+
73 75 
 CHANGES IN VERSION 1.5.4
74 76 
 ------------------------
75 77 
  o reroot method for raxml object <2016-05-22, Sun>
... ... 
@@ -77,7 +79,7 @@ CHANGES IN VERSION 1.5.4
77 79 
  o bug fixed in collapse <2016-05-20, Fri>
78 80 
    + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
79 81 
  o use byte compiler <2016-05-18, Wed>
80 
- o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
82 
+ o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
81 83 
  o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106
82 84
83 85 
 CHANGES IN VERSION 1.5.3
... ... 
@@ -86,9 +88,9 @@ CHANGES IN VERSION 1.5.3
86 88 
    + add fan layout example in treeVisualization vignette
87 89 
    + add open_tree and rotate_tree example in treeManipulation vignette
88 90 
  o add angle in ggtree function, fan layout supported <2016-05-12, Thu>
89 
- o rotate_tree and open_tree function <2016-05-12, Thu>
91 
+ o rotate_tree and open_tree function <2016-05-12, Thu>
90 92 
  o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <2016-05-12, Thu>
91 
- o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5
93 
+ o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5
92 94
93 95 
 CHANGES IN VERSION 1.5.2
94 96 
 ------------------------
... ... 
@@ -101,7 +103,7 @@ CHANGES IN VERSION 1.5.2
101 103 
    + https://github.com/GuangchuangYu/ggtree/issues/40
102 104 
  o supports phylo4d object <2016-05-10, Tue>
103 105 
    + https://github.com/GuangchuangYu/ggtree/issues/47
104 
-
106 
+
105 107 
 CHANGES IN VERSION 1.5.1
106 108 
 ------------------------
107 109 
  o update vignettes <2016-05-10, Tue>
... ... 
@@ -113,11 +115,11 @@ CHANGES IN VERSION 1.5.1
113 115 
    + https://github.com/GuangchuangYu/ggtree/pull/57
114 116 
  o geom_strip for associated taxa <2016-05-09, Mon>
115 117 
    + https://github.com/GuangchuangYu/ggtree/issues/52
116 
-
118 
+
117 119 
 CHANGES IN VERSION 1.4.0
118 120 
 ------------------------
119 121 
  o BioC 3.3 released <2016-05-05, Thu>
120 
-
122 
+
121 123 
 CHANGES IN VERSION 1.3.16
122 124 
 ------------------------
123 125 
  o geom_treescale() supports family argument <2016-04-27, Wed>
... ... 
@@ -127,7 +129,7 @@ CHANGES IN VERSION 1.3.16
127 129 
  o support passing textConnection(text_string) as a file <2016-04-21, Thu>
128 130 
    + contributed by Casey Dunn <casey_dunn@brown.edu>
129 131 
    + https://github.com/GuangchuangYu/ggtree/pull/55#issuecomment-212859693
130 
-
132 
+
131 133 
 CHANGES IN VERSION 1.3.15
132 134 
 ------------------------
133 135 
  o geom_tiplab2 supports parameter hjust <2016-04-18, Mon>
... ... 
@@ -135,9 +137,9 @@ CHANGES IN VERSION 1.3.15
135 137 
  o geom_label2 that support subsetting <2016-04-07, Thu>
136 138 
  o geom_tiplab2 for adding tip label of circular layout <2016-04-06, Wed>
137 139 
  o use plot$plot_env to access ggplot2 parameter <2016-04-06, Wed>
138 
- o geom_taxalink for connecting related taxa <2016-04-01, Fri>
140 
+ o geom_taxalink for connecting related taxa <2016-04-01, Fri>
139 141 
  o geom_range for adding range of HPD to present uncertainty of evolutionary inference <2016-04-01, Fri>
140 
-
142 
+
141 143 
 CHANGES IN VERSION 1.3.14
142 144 
 ------------------------
143 145 
  o geom_tiplab works with NA values, compatible with collapse <2016-03-05, Sat>
... ... 
@@ -145,12 +147,12 @@ CHANGES IN VERSION 1.3.14
145 147 
  o offset works in `align=FFALSE` with `annotation_image` function <2016-02-23, Tue>
146 148 
    + see https://github.com/GuangchuangYu/ggtree/issues/46
147 149 
  o subview and inset now supports annotating with img files <2016-02-23, Tue>
148 
-
150 
+
149 151 
 CHANGES IN VERSION 1.3.13
150 152 
 ------------------------
151 153 
  o add example of rescale_tree function in treeAnnotation.Rmd <2016-02-07, Sun>
152 154 
  o geom_cladelabel works with collapse <2016-02-07, Sun>
153 
-   + see https://github.com/GuangchuangYu/ggtree/issues/38
155 
+   + see https://github.com/GuangchuangYu/ggtree/issues/38
154 156
155 157 
 CHANGES IN VERSION 1.3.12
156 158 
 ------------------------
... ... 
@@ -158,8 +160,8 @@ CHANGES IN VERSION 1.3.12
158 160 
  o solved issues of geom_tree2 <2016-01-25, Mon>
159 161 
    + https://github.com/hadley/ggplot2/issues/1512
160 162 
  o colnames_level parameter in gheatmap <2016-01-25, Mon>
161 
- o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
162 
-
163 
+ o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
164 
+
163 165 
 CHANGES IN VERSION 1.3.11
164 166 
 ------------------------
165 167 
  o solved issues of geom_tree2 <2016-01-25, Mon>
... ... 
@@ -171,7 +173,7 @@ CHANGES IN VERSION 1.3.11
171 173 
  o implement geom_tree2 layer that support duplicated node records via the setup_tree_data function <2016-01-21, Thu>
172 174 
  o rescale_tree function for rescaling branch length of tree object <2016-01-20, Wed>
173 175 
  o upgrade set_branch_length, now branch can be rescaled using feature in extraInfo slot <2016-01-20, Wed>
174 
-
176 
+
175 177 
 CHANGES IN VERSION 1.3.10
176 178 
 ------------------------
177 179 
  o remove dependency of gridExtra by implementing multiplot function instead of using grid.arrange <2016-01-20, Wed>
... ... 
@@ -185,7 +187,7 @@ CHANGES IN VERSION 1.3.9
185 187 
  o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.
186 188 
    these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>
187 189 
    + > ggtree(rtree(30)); viewClade(node=35) works. no need to pipe.
188 
-
190 
+
189 191 
 CHANGES IN VERSION 1.3.8
190 192 
 ------------------------
191 193 
  o add example of viewClade in 'Tree Manipulation' vignette <2016-01-13, Wed>
... ... 
@@ -195,7 +197,7 @@ CHANGES IN VERSION 1.3.8
195 197 
  o 05 advance tree annotation vignette <2016-01-04, Mon>
196 198 
  o export theme_inset <2016-01-04, Mon>
197 199 
  o inset, nodebar, nodepie functions <2015-12-31, Thu>
198 
-
200 
+
199 201 
 CHANGES IN VERSION 1.3.7
200 202 
 ------------------------
201 203 
  o split the long vignette to several vignettes
... ... 
@@ -204,14 +206,14 @@ CHANGES IN VERSION 1.3.7
204 206 
    + 02 tree visualization <2015-12-28, Mon>
205 207 
    + 03 tree manipulation <2015-12-28, Mon>
206 208 
    + 04 tree annotation <2015-12-29, Tue>
207 
-
209 
+
208 210 
 CHANGES IN VERSION 1.3.6
209 211 
 ------------------------
210 212 
  o MRCA function for finding Most Recent Common Ancestor among a vector of tips <2015-12-22, Tue>
211 213 
  o geom_cladelabel: add bar and label to annotate a clade <2015-12-21, Mon>
212 214 
    - remove annotation_clade and annotation_clade2 functions.
213 215 
  o geom_treescale: tree scale layer. (add_legend was removed) <2015-12-21, Mon>
214 
-
216 
+
215 217 
 CHANGES IN VERSION 1.3.5
216 218 
 ------------------------
217 219 
  o bug fixed, read.nhx now works with scientific notation <2015-11-30, Mon>
... ... 
@@ -226,12 +228,12 @@ CHANGES IN VERSION 1.3.4
226 228 
    + see https://github.com/GuangchuangYu/ggtree/issues/26
227 229 
  o support NHX (New Hampshire X) format via read.nhx function <2015-11-17, Tue>
228 230 
  o bug fixed in extract.treeinfo.jplace <2015-11-17, Thu>
229 
-
231 
+
230 232 
 CHANGES IN VERSION 1.3.3
231 233 
 ------------------------
232 234 
  o support color=NULL in gheatmap, then no colored line will draw within the heatmap <2015-10-30, Fri>
233 235 
  o add `angle` for also rectangular, so that it will be available for layout='rectangular' following by coord_polar() <2015-10-27, Tue>
234 
-
236 
+
235 237 
 CHANGES IN VERSION 1.3.2
236 238 
 ------------------------
237 239 
  o update vignette, add example of ape bootstrap and phangorn ancestral sequences <2015-10-26, Mon>
... ... 
@@ -239,7 +241,7 @@ CHANGES IN VERSION 1.3.2
239 241 
    see https://github.com/GuangchuangYu/ggtree/issues/20
240 242 
  o add support of ancestral sequences inferred by phangorn <2015-10-26, Mon>
241 243 
    see https://github.com/GuangchuangYu/ggtree/issues/21
242 
-
244 
+
243 245 
 CHANGES IN VERSION 1.3.1
244 246 
 ------------------------
245 247 
  o change angle to angle + 90, so that label will in radial direction <2015-10-22, Thu>
... ... 
@@ -247,17 +249,17 @@ CHANGES IN VERSION 1.3.1
247 249 
  o na.rm should be always passed to layer(), fixed it in geom_hilight and geom_text2 <2015-10-21, Wed>
248 250 
    + see https://github.com/hadley/ggplot2/issues/1380
249 251 
  o matching beast stats with tree using internal node number instead of label <2015-10-20, Tue>
250 
-
252 
+
251 253 
 CHANGES IN VERSION 1.2.0
252 254 
 ------------------------
253 255 
  o BioC 3.2 released
254 
-
256 
+
255 257 
 CHANGES IN VERSION 1.1.21
256 258 
 ------------------------
257 259 
  o support hyphy output of ancestral sequences that is in phylip sequential format (no TAXALABELS block available) <2015-10-07, Wed>
258 260 
  o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
259 261 
  o new implementation of geom_hilight, a truly geom layer function <2015-09-10, Thu>
260 
-
262 
+
261 263 
 CHANGES IN VERSION 1.1.20
262 264 
 ------------------------
263 265 
  o bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>
... ... 
@@ -268,7 +270,7 @@ CHANGES IN VERSION 1.1.20
268 270 
    + read.r8s, parser function
269 271 
    + fortify method
270 272 
    + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
271 
- o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
273 
+ o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
272 274 
  o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
273 275 
  o add mrsd parameter for user to specify 'most recent sampling date' for time tree <2015-09-01, Tue>
274 276 
    - remove 'time_scale' parameter.
... ... 
@@ -278,15 +280,15 @@ CHANGES IN VERSION 1.1.20
278 280 
    + plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
279 281 
    + fortify.raxml method
280 282 
  o bug fixed in edgeNum2nodeNum for jplace parsing jplace file <2015-09-01, Tue>
281 
-
283 
+
282 284 
 CHANGES IN VERSION 1.1.19
283 285 
 ------------------------
284 
- o use fortify instead of fortify.phylo in fortify.multiPhylo,
286 
+ o use fortify instead of fortify.phylo in fortify.multiPhylo,
285 287 
    so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon>
286 288 
  o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
287 289 
  o remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon>
288 290 
    + these two packages is not commonly used, and will be loaded automatically when needed.
289 
-
291 
+
290 292 
 CHANGES IN VERSION 1.1.18
291 293 
 ------------------------
292 294 
  o layout name change to 'rectangular', 'slanted', 'circular'/'fan' for phylogram and cladogram (if branch.length = 'none')
... ... 
@@ -294,37 +296,37 @@ CHANGES IN VERSION 1.1.18
294 296 
  o implement geom_point2, geom_text2, geom_segment2 to support subsetting <2015-08-28, Fri>
295 297 
      see https://github.com/hadley/ggplot2/issues/1295
296 298 
  o update geom_tiplab according to geom_text2 and geom_segment2 <2015-08-28, Fri>
297 
- o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
298 
-
299 
+ o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
300 
+
299 301 
 CHANGES IN VERSION 1.1.17
300 302 
 ------------------------
301 303 
  o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>
302 304 
  o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>
303 305 
  o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
304 
- o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
306 
+ o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
305 307 
  o theme_transparent to make background transparent <2015-08-27, Thu>
306 
- o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
307 
-
308 
+ o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
309 
+
308 310 
 CHANGES IN VERSION 1.1.16
309 311 
 ------------------------
310 312 
  o update citation <2015-08-17, Mon>
311 
-
313 
+
312 314 
 CHANGES IN VERSION 1.1.15
313 315 
 ------------------------
314 316 
  o open text angle parameter for annotation_clade/annotation_clade2 <2015-08-13, Thu>
315 317 
  o support changing size of add_legend <2015-08-13, Thu>
316 318 
  o reroot methods for phylo and beast <2015-08-07, Fri>
317 
-
319 
+
318 320 
 CHANGES IN VERSION 1.1.14
319 321 
 ------------------------
320 322 
  o update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available <2015-08-07, Fri>
321 
-
323 
+
322 324 
 CHANGES IN VERSION 1.1.13
323 325 
 ------------------------
324 326 
  o implement annotation_image <2015-08-01, Sat>
325 327 
  o better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat>
326 328 
  o open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat>
327 
-
329 
+
328 330 
 CHANGES IN VERSION 1.1.12
329 331 
 ------------------------
330 332 
  o update vignette according to the changes <2015-07-31, Fri>
... ... 
@@ -332,14 +334,14 @@ CHANGES IN VERSION 1.1.12
332 334 
  o extend groupClade to support operating on tree view <2015-07-31, Fri>
333 335 
  o extend groupOTU to support operating on tree view <2015-07-31, Fri>
334 336 
  o new implementation of groupClade & groupOTU <2015-07-31, Fri>
335 
-
337 
+
336 338 
 CHANGES IN VERSION 1.1.11
337 339 
 ------------------------
338 340 
  o annotation_clade and annotation_clade2 functions. <2015-07-30, Thu>
339 341 
  o better add_legend implementation. <2015-07-30, Thu>
340 342 
  o add ... in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu>
341 343 
  o better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu>
342 
-
344 
+
343 345 
 CHANGES IN VERSION 1.1.10
344 346 
 ------------------------
345 347 
  o solve overlapping branches for layout = "fan" || "radial",
... ... 
@@ -355,32 +357,32 @@ CHANGES IN VERSION 1.1.9
355 357 
  o get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue>
356 358 
  o add example of flip function in vignette <2015-06-30, Tue>
357 359 
  o flip function for exchanging positions of two selected branches <2015-06-30, Tue>
358 
-
360 
+
359 361 
 CHANGES IN VERSION 1.1.8
360 362 
 ------------------------
361 363 
  o update get.placement <2015-06-05, Fri>
362 364 
  o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>
363 365 
  o mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue>
364 366 
  o add mask function <2015-06-02, Tue>
365 
-
367 
+
366 368 
 CHANGES IN VERSION 1.1.7
367 369 
 ------------------------
368 370 
  o add example of msaplot in vignette <2015-05-22, Fri>
369 371 
  o msaplot for adding multiple sequence alignment <2015-05-22, Fri>
370 
-
372 
+
371 373 
 CHANGES IN VERSION 1.1.6
372 374 
 ------------------------
373 375 
  o add vertical_only parameter to scaleClade and set to TRUE by default.
374 376 
    only vertical will be scaled by default. <2015-05-22, Fri>
375 377 
  o update add_colorbar & add_legend <2015-05-21, Thu>
376 
- o add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
378 
+ o add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
377 379 
  o gheatmap implementation of gplot <2015-05-18, Mon>
378 380 
  o add_legend for adding evolution distance legend <2015-05-18, Mon>
379 
-
381 
+
380 382 
 CHANGES IN VERSION 1.1.5
381 383 
 ------------------------
382 384 
  o implement scaleClade <2015-05-12, Tue>
383 
-
385 
+
384 386 
 CHANGES IN VERSION 1.1.4
385 387 
 ------------------------
386 388 
  o better performance of parsing beast tree  <2015-05-11, Mon>
... ... 
@@ -388,13 +390,13 @@ CHANGES IN VERSION 1.1.4
388 390 
    + support file that only contains one evidence for some of the nodes/tips
389 391 
  o update add_colorbar to auto determine the position <2015-05-04, Mon>
390 392 
  o add_colorbar function <2015-04-30, Thu>
391 
-
393 
+
392 394 
 CHANGES IN VERSION 1.1.3
393 395 
 ------------------------
394 396 
  o add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu>
395 397 
  o remove slash line in heatmap legend <2015-04-30, Thu>
396 398 
  o update vignette to add example of merge_tree <2015-04-29, Wed>
397 
-
399 
+
398 400 
 CHANGES IN VERSION 1.1.2
399 401 
 ------------------------
400 402 
  o in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]* <2015-04-29, Wed>
... ... 
@@ -409,17 +411,17 @@ CHANGES IN VERSION 1.1.2
409 411 
  o extend get.fields methods to support additional fields <2015-04-28, Tue>
410 412 
  o extend tree class to support additional info by merging two tree <2015-04-28, Tue>
411 413 
  o implement merge_tree function to merge two tree objects into one <2015-04-28, Tue>
412 
-
414 
+
413 415 
 CHANGES IN VERSION 1.1.1
414 416 
 ------------------------
415 417 
  o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
416 418 
  o update parsing beast time scale tree to support _year (originally supports _year.\\d+) <2015-04-27, Mon>
417 419 
  o add Tommy in author <2015-04-27, Mon>
418 
-
420 
+
419 421 
 CHANGES IN VERSION 0.99.28
420 422 
 ------------------------
421 423 
  o update vignette with floating table of content <2015-04-08, Wed>
422 
-
424 
+
423 425 
 CHANGES IN VERSION 0.99.27
424 426 
 ------------------------
425 427 
  o bug fixed, see https://github.com/GuangchuangYu/ggtree/issues/4 <2015-03-07, Tue>
... ... 
@@ -428,42 +430,42 @@ CHANGES IN VERSION 0.99.26
428 430 
 ------------------------
429 431 
  o update geom_tiplab <2015-03-31, Tue>
430 432 
  o update plot method of beast <2015-03-17, Tue>
431 
-
433 
+
432 434 
 CHANGES IN VERSION 0.99.25
433 435 
 ------------------------
434 436 
  o implement groupClade <2015-03-13, Fri>
435 
-
437 
+
436 438 
 CHANGES IN VERSION 0.99.24
437 439 
 ------------------------
438 440 
  o use "round" segment end, look very better <2015-03-12, Thu>
439 441 
  o update vignett <2015-03-11, Wed>
440 
-
442 
+
441 443 
 CHANGES IN VERSION 0.99.23
442 444 
 ------------------------
443 445 
  o mv geom_hilight to hilight <2015-03-11, Wed>
444 446 
  o mv geom_phylopic to phylopic <2015-03-11, Wed>
445 
- o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
446 
-
447 
+ o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
448 
+
447 449 
 CHANGES IN VERSION 0.99.22
448 450 
 ------------------------
449 451 
  o remove quote in beast tip/node labels <2015-03-10, Tue>
450 
-
452 
+
451 453 
 CHANGES IN VERSION 0.99.21
452 454 
 ------------------------
453 455 
  o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue>
454 
-
456 
+
455 457 
 CHANGES IN VERSION 0.99.19
456 458 
 ------------------------
457 459 
  o for time scale tree inferred by BEAST, now user can use time_scale=TRUE parameter in ggtree function <2015-02-12, Thu>
458 
-
460 
+
459 461 
 CHANGES IN VERSION 0.99.18
460 462 
 ------------------------
461 463 
  o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu>
462 
-
464 
+
463 465 
 CHANGES IN VERSION 0.99.17
464 466 
 ------------------------
465 467 
  o add angle and branch.y variable in cladogram layout <2015-02-10, Tue>
466 
-
468 
+
467 469 
 CHANGES IN VERSION 0.99.16
468 470 
 ------------------------
469 471 
  o correct typo in vignette <2015-02-10, Tue>
... ... 
@@ -471,7 +473,7 @@ CHANGES IN VERSION 0.99.16
471 473 
 CHANGES IN VERSION 0.99.15
472 474 
 ------------------------
473 475 
  o fully support of replace operator, %<% <2015-02-09, Mon>
474 
-
476 
+
475 477 
 CHANGES IN VERSION 0.99.14
476 478 
 ------------------------
477 479 
  o add example in groupOTU for adding legend manually <2015-02-09, Mon>.
... ... 
@@ -479,13 +481,13 @@ CHANGES IN VERSION 0.99.14
479 481 
 CHANGES IN VERSION 0.99.13
480 482 
 ------------------------
481 483 
  o two dimensional tree <2015-02-06, Fri>
482 
-
484 
+
483 485 
 CHANGES IN VERSION 0.99.12
484 486 
 ------------------------
485 487 
  o update vignette <2015-02-04, Wed>
486 488 
  o gzoom methods that supports all tree objects <2015-02-04, Wed>
487 
- o geom_hilight layer for highlighting clade <2015-02-04, Wed>
488 
-
489 
+ o geom_hilight layer for highlighting clade <2015-02-04, Wed>
490 
+
489 491 
 CHANGES IN VERSION 0.99.11
490 492 
 ------------------------
491 493 
  o add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed>
... ... 
@@ -499,12 +501,12 @@ CHANGES IN VERSION 0.99.10
499 501 
 CHANGES IN VERSION 0.99.9
500 502 
 ------------------------
501 503 
  o update vignette <2015-02-02, Mon>
502 
-
504 
+
503 505 
 CHANGES IN VERSION 0.99.8
504 506 
 ------------------------
505 507 
  o add get.phylopic function to read the online phylo pic and convert it to grob object,
506 508 
    which can be use to annotate ggplot figure using annotation_custom <2015-01-30, Fri>
507 
-
509 
+
508 510 
 CHANGES IN VERSION 0.99.7
509 511 
 ------------------------
510 512 
  o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu>
... ... 
@@ -513,7 +515,7 @@ CHANGES IN VERSION 0.99.6
513 515 
 ------------------------
514 516 
  o read.beast now supports support values of sets such as {x, y, z} <2015-01-19, Mon>
515 517 
  o now read.beast supports characters in support values <2015-01-18, Sun>
516 
- o add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
518 
+ o add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
517 519 
  o implement groupOTU methods <2015-01-14, Wed>
518 520 
  o export get.offspring.tip <2015-01-14, Wed>
519 521
... ... 
@@ -524,7 +526,7 @@ CHANGES IN VERSION 0.99.5
524 526 
  o add gzoom function, similar to zoom function in ape <2015-01-07, Wed>
525 527 
  o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>
526 528 
  o remove <<- and update vignette <2015-01-06, Tue>
527 
- o update vignette and use BibTex and CSL for references <2015-01-05, Mon>
529 
+ o update vignette and use BibTex and CSL for references <2015-01-05, Mon>
528 530 
  o update cladogram layout <2015-01-05, Mon>
529 531 
  o read.baseml function and update vignette with baseml example <2015-01-04, Sun>
530 532 
  o plot method for hyphy and hyphy example in vignette <2015-01-04, Sun>
... ... 
@@ -532,9 +534,9 @@ CHANGES IN VERSION 0.99.5
532 534
533 535 
 CHANGES IN VERSION 0.99.4
534 536 
 ------------------------
535 
- o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat>
537 
+ o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat>
536 538 
  o get.subs method for hyphy object <2015-01-03, Sat>
537 
- o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
539 
+ o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
538 540 
  o export read.hyphy <2015-01-02, Fri>
539 541 
  o export hyphy class <2015-01-01, Thu>
540 542 
  o plot method for beast class and get.tree method for codeml class <2014-12-31, Wed>
... ... 
@@ -547,7 +549,7 @@ CHANGES IN VERSION 0.99.4
547 549 
  o update man file and add example file of beast output <2014-12-26, Fri>
548 550 
  o get.tree and get.fileds methods of beast class <2014-12-26, Fri>
549 551 
  o read.beast <2014-12-26, Fri>
550 
- o beast class and show method <2014-12-26, Fri>
552 
+ o beast class and show method <2014-12-26, Fri>
551 553 
  o coplot prototype<2014-12-24, Wed>
552 554 
  o parse translation matrix in beast nexus <2014-12-24, Wed>
553 555 
  o extract beast stats info <2014-12-23, Tue>
... ... 
@@ -560,7 +562,7 @@ CHANGES IN VERSION 0.99.3
560 562 
  o write.jplace and fully supports of jplace by ggtree. <2014-12-21, Sun>
561 563 
  o support unrooted layout in ggplot. <2014-12-21, Sun>
562 564 
  o support fan, radial, dendrogram layout in geom_tree. <2014-12-21, Sun>
563 
-
565 
+
564 566 
 CHANGES IN VERSION 0.99.2
565 567 
 ------------------------
566 568 
  o layout of unrooted tree, implemented equal-angle algorithm that described in Chapter 34
Browse code

as.polytomy

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@121115 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 19/09/2016 07:21:18
Showing1 changed files
NEWS
History View file @215c8da9
... ... 
@@ -1,3 +1,10 @@
1 
+CHANGES IN VERSION 1.5.14
2 
+------------------------
3 
+ o update angle calculation for geom_tiplab <2016-09-13, Thu>
4 
+ o as.polytomy to collapse binary tree to polytomy by applying 'fun' to selected 'feature' (e.g. bootstrap value less than 70). <2016-09-13, Tue>
5 
+   + currently only phylo object supported.
6 
+   + add test for as.polytomy
7 
+
1 8 
 CHANGES IN VERSION 1.5.13
2 9 
 ------------------------
3 10 
  o facet_plot for plotting data with tree <2016-09-06, Tue>
Browse code

facet_plot

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120776 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 07/09/2016 01:36:05
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History View file @90c9d156
... ... 
@@ -1,5 +1,16 @@
1 
+CHANGES IN VERSION 1.5.13
2 
+------------------------
3 
+ o facet_plot for plotting data with tree <2016-09-06, Tue>
4 
+ o more parameters for column names in gheatmap <2016-09-06, Tue>
5 
+   + colnames_angle
6 
+   + colnames_offset_x
7 
+   + colnames_offset_y
8 
+   + hjust
9 
+ o offset parameter in geom_tiplab and geom_tiplab2 <2016-09-05, Mon>
10 
+
1 11 
 CHANGES IN VERSION 1.5.12
2 12 
 ------------------------
13 
+ o use data in all layers instead of the base layer for coordination calculation in subview <2016-09-01, Thu>
3 14 
  o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
4 15
5 16 
 CHANGES IN VERSION 1.5.11
Browse code

bug fixed in subview

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120638 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 01/09/2016 03:51:25
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History View file @138649a5
... ... 
@@ -1,3 +1,7 @@
1 
+CHANGES IN VERSION 1.5.12
2 
+------------------------
3 
+ o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
4 
+
1 5 
 CHANGES IN VERSION 1.5.11
2 6 
 ------------------------
3 7 
  o gheatmap works with matrix <2016-08-28, Sun>
Browse code

update docs

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120612 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 31/08/2016 06:22:59
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History View file @410f5ad6
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@@ -1,5 +1,8 @@
1 1 
 CHANGES IN VERSION 1.5.11
2 2 
 ------------------------
3 
+ o gheatmap works with matrix <2016-08-28, Sun>
4 
+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/2YLvXHMJJ6U/c4zS7yfGCAAJ
5 
+ o support parsing expression in geom_strip <2016-08-18, Thu>
3 6 
  o bug fixed in geom_tiplab <2016-08-17, Wed>
4 7 
    + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
5 8 
  o update citation info, add doi. <2016-08-16, Tue>
Browse code

citation info with doi

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120192 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 17/08/2016 05:42:13
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History View file @567ab02f
... ... 
@@ -1,3 +1,9 @@
1 
+CHANGES IN VERSION 1.5.11
2 
+------------------------
3 
+ o bug fixed in geom_tiplab <2016-08-17, Wed>
4 
+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
5 
+ o update citation info, add doi. <2016-08-16, Tue>
6 
+
1 7 
 CHANGES IN VERSION 1.5.10
2 8 
 ------------------------
3 9 
  o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
Browse code

bug fixed in geom_treescale

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120154 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 16/08/2016 04:18:17
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History View file @17714487
... ... 
@@ -1,3 +1,8 @@
1 
+CHANGES IN VERSION 1.5.10
2 
+------------------------
3 
+ o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
4 
+   + https://github.com/GuangchuangYu/ggtree/issues/72
5 
+
1 6 
 CHANGES IN VERSION 1.5.9
2 7 
 ------------------------
3 8 
  o update citation info <2016-08-12, Fri>
Browse code

update citation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120063 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 12/08/2016 02:34:40
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History View file @5540ce8d
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@@ -1,3 +1,7 @@
1 
+CHANGES IN VERSION 1.5.9
2 
+------------------------
3 
+ o update citation info <2016-08-12, Fri>
4 
+
1 5 
 CHANGES IN VERSION 1.5.8
2 6 
 ------------------------
3 7 
  o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
Browse code

geom_cladelabel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120045 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 11/08/2016 06:54:44
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History View file @5662ae9e
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@@ -1,3 +1,8 @@
1 
+CHANGES IN VERSION 1.5.8
2 
+------------------------
3 
+ o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
4 
+ o geom_cladelabel support parsing expression <2016-08-11, Thu>
5 
+
1 6 
 CHANGES IN VERSION 1.5.7
2 7 
 ------------------------
3 8 
  o geom_strip can accept taxa name as input but labeling strip will not supported.
Browse code

update geom_strip

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@119677 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 27/07/2016 05:17:32
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History View file @6d2be639
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@@ -1,6 +1,7 @@
1 1 
 CHANGES IN VERSION 1.5.7
2 2 
 ------------------------
3 
- o geom_strip now only accept node id as input and support labeling strip <2016-07-27, Wed>
3 
+ o geom_strip can accept taxa name as input but labeling strip will not supported.
4 
+   To support labeling strip, user need to input node id  <2016-07-27, Wed>
4 5 
  o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
5 6
6 7 
 CHANGES IN VERSION 1.5.6
Browse code

update geom_strip and add nodeid function

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@119673 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 27/07/2016 04:22:44
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History View file @84e78228
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@@ -1,3 +1,8 @@
1 
+CHANGES IN VERSION 1.5.7
2 
+------------------------
3 
+ o geom_strip now only accept node id as input and support labeling strip <2016-07-27, Wed>
4 
+ o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
5 
+
1 6 
 CHANGES IN VERSION 1.5.6
2 7 
 ------------------------
3 8 
  o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
Browse code

clean dependencies

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@119521 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 21/07/2016 13:16:38
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History View file @27786944
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@@ -1,5 +1,11 @@
1 1 
 CHANGES IN VERSION 1.5.6
2 2 
 ------------------------
3 
+ o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
4 
+   + still needed for building vignette and for processing FASTA file
5 
+ o remove dependency of EBImage for building & installing ggtree <2016-07-21, Thu>
6 
+   + the package is still needed if user want to annotate tree with image file
7 
+ o `%<+%` now works with tbl_df <2016-07-21, Thu>
8 
+   + https://github.com/GuangchuangYu/ggtree/issues/66
3 9 
  o identify method for ggtree <2016-06-28, Tue>
4 10 
    + see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree
5 11 
  o geom_balance contributed by Justin Silverman <2016-06-22, Wed>
Browse code

update docs

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@119011 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 29/06/2016 03:33:31
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History View file @3a0dfc07
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@@ -1,5 +1,7 @@
1 1 
 CHANGES IN VERSION 1.5.6
2 2 
 ------------------------
3 
+ o identify method for ggtree <2016-06-28, Tue>
4 
+   + see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree
3 5 
  o geom_balance contributed by Justin Silverman <2016-06-22, Wed>
4 6 
    + see https://github.com/GuangchuangYu/ggtree/pull/64
5 7
Browse code

update citation info

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118925 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 24/06/2016 06:22:28
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History View file @13e3fd30
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@@ -1,3 +1,8 @@
1 
+CHANGES IN VERSION 1.5.6
2 
+------------------------
3 
+ o geom_balance contributed by Justin Silverman <2016-06-22, Wed>
4 
+   + see https://github.com/GuangchuangYu/ggtree/pull/64
5 
+
1 6 
 CHANGES IN VERSION 1.5.5
2 7 
 ------------------------
3 8 
  o update geom_tiplab2 according to angle change introduced by open_tree <2016-06-20, Mon>
Browse code

update geom_tiplab2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118763 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 20/06/2016 06:20:08
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History View file @4a860280
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@@ -1,5 +1,6 @@
1 1 
 CHANGES IN VERSION 1.5.5
2 2 
 ------------------------
3 
+ o update geom_tiplab2 according to angle change introduced by open_tree <2016-06-20, Mon>
3 4 
  o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu>
4 5 
  o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
5 6 
    + as.Date won't work for BCE time.
Browse code

bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118094 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 02/06/2016 03:29:16
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History View file @57e5e2f6
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@@ -1,5 +1,6 @@
1 1 
 CHANGES IN VERSION 1.5.5
2 2 
 ------------------------
3 
+ o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu>
3 4 
  o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
4 5 
    + as.Date won't work for BCE time.
5 6 
    + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
Browse code

version 1.5.5

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118092 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 02/06/2016 03:14:43
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History View file @328fdc06
... ... 
@@ -1,5 +1,12 @@
1 
+CHANGES IN VERSION 1.5.5
2 
+------------------------
3 
+ o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
4 
+   + as.Date won't work for BCE time.
5 
+   + as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
6 
+
1 7 
 CHANGES IN VERSION 1.5.4
2 8 
 ------------------------
9 
+ o reroot method for raxml object <2016-05-22, Sun>
3 10 
  o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>
4 11 
  o bug fixed in collapse <2016-05-20, Fri>
5 12 
    + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
Browse code

bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117703 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 20/05/2016 06:35:51
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History View file @77debaae
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1 1 
 CHANGES IN VERSION 1.5.4
2 2 
 ------------------------
3 
+ o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>
3 4 
  o bug fixed in collapse <2016-05-20, Fri>
4 5 
    + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
5 6 
  o use byte compiler <2016-05-18, Wed>
Browse code

bug fixed in collapse

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117702 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 20/05/2016 06:04:12
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History View file @140b3239
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1 1 
 CHANGES IN VERSION 1.5.4
2 2 
 ------------------------
3 
+ o bug fixed in collapse <2016-05-20, Fri>
4 
+   + if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
3 5 
  o use byte compiler <2016-05-18, Wed>
4 6 
  o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
5 7 
  o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106
Browse code

byte compiler

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117653 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 19/05/2016 01:22:50
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