guangchuang yu authored on 14/12/2017 10:29:44
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.11.3 |
| 2 | 2 |
------------------------ |
| 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 |
|
guangchuang yu authored on 14/12/2017 08:47:21
guangchuang yu authored on 07/12/2017 07:21:58
| ... | ... |
@@ -1,3 +1,7 @@ |
| 1 |
+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> |
guangchuang yu authored on 06/12/2017 02:01:19
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.11.2 |
| 2 | 2 |
------------------------ |
| 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> |
guangchuang yu authored on 05/12/2017 11:05:11
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.11.2 |
| 2 | 2 |
------------------------ |
| 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> |
guangchuang yu authored on 04/12/2017 12:41:52
| ... | ... |
@@ -1,6 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.11.2 |
| 2 | 2 |
------------------------ |
| 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 |
|
guangchuang yu authored on 04/12/2017 11:45:07
| ... | ... |
@@ -1,3 +1,9 @@ |
| 1 |
+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> |
guangchuang yu authored on 20/11/2017 13:20:02
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.11.1 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
guangchuang yu authored on 15/11/2017 07:45:39
| ... | ... |
@@ -1,3 +1,9 @@ |
| 1 |
+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 |
|
| 6 |
+ |
|
| 1 | 7 |
CHANGES IN VERSION 1.9.4 |
| 2 | 8 |
------------------------ |
| 3 | 9 |
o geom_hilight_encircle and geom_cladelabel2 <2017-09-12, Tue> |
guangchuang yu authored on 12/09/2017 10:01:00
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.4 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
guangchuang yu authored on 30/08/2017 06:34:31
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.4 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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> |
guangchuang yu authored on 22/08/2017 08:22:37
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.4 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
guangchuang yu authored on 22/08/2017 06:08:09
| ... | ... |
@@ -1,3 +1,7 @@ |
| 1 |
+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> |
guangchuang yu authored on 03/08/2017 05:05:40
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.3 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
|
guangchuang yu authored on 01/08/2017 12:22:46
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.3 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
guangchuang yu authored on 27/07/2017 03:46:36
guangchuang yu authored on 26/07/2017 07:46:20
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.2 |
| 2 | 2 |
------------------------ |
| 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> |
guangchuang yu authored on 26/07/2017 02:13:53
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.2 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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> |
guangchuang yu authored on 20/07/2017 07:44:44
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.2 |
| 2 | 2 |
------------------------ |
| 3 |
+ o scaleClade works after calling viewClade <2017-07-20, Thu> |
|
| 4 |
+ + 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 |
|
guangchuang yu authored on 29/06/2017 05:10:11
| ... | ... |
@@ -1,3 +1,8 @@ |
| 1 |
+CHANGES IN VERSION 1.9.2 |
|
| 2 |
+------------------------ |
|
| 3 |
+ o gheatmap support handling collapsed tree <2017-06-29, Thu> |
|
| 4 |
+ + https://github.com/GuangchuangYu/ggtree/issues/137 |
|
| 5 |
+ |
|
| 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> |
guangchuang yu authored on 19/06/2017 13:28:29
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.1 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
GuangchuangYu authored on 05/05/2017 21:01:50
guangchuang yu authored on 27/04/2017 07:25:59
guangchuang yu authored on 20/04/2017 02:28:57
| ... | ... |
@@ -1,3 +1,9 @@ |
| 1 |
+CHANGES IN VERSION 1.7.11 |
|
| 2 |
+------------------------ |
|
| 3 |
+ o remove layout.method parameter <2017-04-20, Thu> |
|
| 4 |
+ + https://github.com/GuangchuangYu/ggtree/issues/118#issuecomment-295130818 |
|
| 5 |
+ + https://github.com/GuangchuangYu/ggtree/issues/125 |
|
| 6 |
+ |
|
| 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> |
guangchuang yu authored on 23/03/2017 03:40:26
| ... | ... |
@@ -1,5 +1,8 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.10 |
| 2 | 2 |
------------------------ |
| 3 |
+ o add message for subview, inset, phylopic, theme_transparent and theme_inset <2017-03-23, Thu> |
|
| 4 |
+ + will be defunct in version >= 1.9.0 |
|
| 5 |
+ + 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 |
guangchuang yu authored on 13/03/2017 05:39:11
| ... | ... |
@@ -1,3 +1,7 @@ |
| 1 |
+CHANGES IN VERSION 1.7.10 |
|
| 2 |
+------------------------ |
|
| 3 |
+ o update subview to support mainview produced by `ggplot() + layers` <2017-03-13, Mon> |
|
| 4 |
+ |
|
| 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> |
guangchuang yu authored on 03/03/2017 05:42:32
guangchuang yu authored on 02/03/2017 02:49:53
| ... | ... |
@@ -1,3 +1,8 @@ |
| 1 |
+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 |
|
| 5 |
+ |
|
| 1 | 6 |
CHANGES IN VERSION 1.7.8 |
| 2 | 7 |
------------------------ |
| 3 | 8 |
o get_taxa_name now sorted by taxa position and also support whole tree <2017-03-01, Wed> |
guangchuang yu authored on 01/03/2017 08:49:58
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.8 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
guangchuang yu authored on 28/02/2017 07:11:57
| ... | ... |
@@ -1,3 +1,7 @@ |
| 1 |
+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> |
|
| 4 |
+ |
|
| 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> |
guangchuang yu authored on 16/02/2017 06:54:38
| ... | ... |
@@ -1,6 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.7 |
| 2 | 2 |
------------------------ |
| 3 |
- 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> |
guangchuang yu authored on 16/02/2017 06:10:17
| ... | ... |
@@ -1,9 +1,11 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.7 |
| 2 | 2 |
------------------------ |
| 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 |
------------------------ |
| 9 | 11 |
o inset support reverse scale <2017-01-05, Thu> |
guangchuang yu authored on 13/02/2017 05:33:14
GuangchuangYu authored on 20/01/2017 05:21:52
guangchuang yu authored on 05/01/2017 03:23:11
| ... | ... |
@@ -1,3 +1,8 @@ |
| 1 |
+CHANGES IN VERSION 1.7.6 |
|
| 2 |
+------------------------ |
|
| 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 |
|
| 5 |
+ |
|
| 1 | 6 |
CHANGES IN VERSION 1.7.5 |
| 2 | 7 |
------------------------ |
| 3 | 8 |
o disable labeling collapsed node as tip <2017-01-03, Tue> |
guangchuang yu authored on 03/01/2017 03:47:16
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.5 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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> |
guangchuang yu authored on 28/12/2016 13:49:47
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.5 |
| 2 | 2 |
------------------------ |
| 3 |
+ 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 |
|
guangchuang yu authored on 28/12/2016 08:08:07
| ... | ... |
@@ -1,7 +1,8 @@ |
| 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> |
GuangchuangYu authored on 20/12/2016 16:39:07
| ... | ... |
@@ -1,3 +1,7 @@ |
| 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> |
guangchuang yu authored on 06/12/2016 07:53:23
| ... | ... |
@@ -1,5 +1,6 @@ |
| 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> |
guangchuang yu authored on 06/12/2016 05:42:11
| ... | ... |
@@ -1,5 +1,6 @@ |
| 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> |
guangchuang yu authored on 01/12/2016 04:40:01
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.4 |
| 2 | 2 |
------------------------ |
| 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 |
guangchuang yu authored on 28/11/2016 05:42:43
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.4 |
| 2 | 2 |
------------------------ |
| 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>
|
guangchuang yu authored on 24/11/2016 05:04:08
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.7.4 |
| 2 | 2 |
------------------------ |
| 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 |
|
guangchuang yu authored on 16/11/2016 05:54:24
| ... | ... |
@@ -1,3 +1,8 @@ |
| 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> |
guangchuang yu authored on 11/11/2016 05:33:47
guangchuang yu authored on 09/11/2016 08:00:46
guangchuang yu authored on 07/11/2016 03:16:33
| ... | ... |
@@ -1,3 +1,8 @@ |
| 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> |
GuangchuangYu authored on 03/11/2016 15:30:13
| ... | ... |
@@ -1,5 +1,6 @@ |
| 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> |
guangchuang yu authored on 01/11/2016 02:38:09
| ... | ... |
@@ -1,7 +1,7 @@ |
| 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 |
|
guangchuang yu authored on 01/11/2016 02:23:02
| ... | ... |
@@ -1,12 +1,14 @@ |
| 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 |
guangchuang yu authored on 31/10/2016 11:29:54
| ... | ... |
@@ -1,3 +1,8 @@ |
| 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> |
guangchuang yu authored on 31/10/2016 07:41:12
| ... | ... |
@@ -1,6 +1,6 @@ |
| 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 |
guangchuang yu authored on 31/10/2016 04:10:22
| ... | ... |
@@ -1,5 +1,11 @@ |
| 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> |
guangchuang yu authored on 26/10/2016 08:27:56
guangchuang yu authored on 24/10/2016 07:52:43
| ... | ... |
@@ -1,7 +1,11 @@ |
| 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> |
guangchuang yu authored on 18/10/2016 01:23:55
guangchuang yu authored on 17/10/2016 03:02:31
| ... | ... |
@@ -1,3 +1,8 @@ |
| 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> |
guangchuang yu authored on 11/10/2016 10:02:10
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.5.16 |
| 2 | 2 |
------------------------ |
| 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 |
guangchuang yu authored on 11/10/2016 06:41:22
| ... | ... |
@@ -1,8 +1,9 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.5.16 |
| 2 | 2 |
------------------------ |
| 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> |
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
| ... | ... |
@@ -1,3 +1,8 @@ |
| 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> |
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
| ... | ... |
@@ -1,3 +1,9 @@ |
| 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> |
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
| ... | ... |
@@ -1,5 +1,6 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.5.14 |
| 2 | 2 |
------------------------ |
| 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> |
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
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.5.14 |
| 2 | 2 |
------------------------ |
| 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> |
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
| ... | ... |
@@ -1,10 +1,12 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.5.14 |
| 2 | 2 |
------------------------ |
| 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> |
| ... | ... |
@@ -14,12 +16,12 @@ CHANGES IN VERSION 1.5.13 |
| 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> |
| ... | ... |
@@ -28,27 +30,27 @@ CHANGES IN VERSION 1.5.11 |
| 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> |
| ... | ... |
@@ -69,7 +71,7 @@ CHANGES IN VERSION 1.5.5 |
| 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 < |