Browse code

update msaplot to use DNAbin/AAbin

guangchuang yu authored on 14/12/2017 10:29:44
Showing1 changed files
... ...
@@ -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
 
Browse code

clean up code

guangchuang yu authored on 14/12/2017 08:47:21
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
1 1
 CHANGES IN VERSION 1.11.3
2 2
 ------------------------
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
Showing1 changed files
... ...
@@ -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>
Browse code

keep tree order #157

guangchuang yu authored on 06/12/2017 02:01:19
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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>
Browse code

remove theme_transparent

guangchuang yu authored on 04/12/2017 12:41:52
Showing1 changed files
... ...
@@ -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
 
Browse code

ggtree with image files

guangchuang yu authored on 04/12/2017 11:45:07
Showing1 changed files
... ...
@@ -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>
Browse code

geom_tiplab enhancement

guangchuang yu authored on 20/11/2017 13:20:02
Showing1 changed files
... ...
@@ -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
Browse code

mrsd for treedata object

guangchuang yu authored on 15/11/2017 07:45:39
Showing1 changed files
... ...
@@ -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>
Browse code

fixed R check for #152

guangchuang yu authored on 12/09/2017 10:01:00
Showing1 changed files
... ...
@@ -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
Browse code

set_hilight_legend

guangchuang yu authored on 30/08/2017 06:34:31
Showing1 changed files
... ...
@@ -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>
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing1 changed files
... ...
@@ -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
Browse code

update docs

guangchuang yu authored on 22/08/2017 06:08:09
Showing1 changed files
... ...
@@ -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>
Browse code

compatible with tidyr 0.7.0

guangchuang yu authored on 03/08/2017 05:05:40
Showing1 changed files
... ...
@@ -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
 
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
Showing1 changed files
... ...
@@ -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
Browse code

jplace

guangchuang yu authored on 27/07/2017 03:46:36
Showing1 changed files
... ...
@@ -1,3 +1,7 @@
1
+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
 ------------------------
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
Showing1 changed files
... ...
@@ -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>
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing1 changed files
... ...
@@ -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>
Browse code

scaleClade works after calling viewClade

guangchuang yu authored on 20/07/2017 07:44:44
Showing1 changed files
... ...
@@ -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
 
Browse code

gheatmap supports collapsed tree

guangchuang yu authored on 29/06/2017 05:10:11
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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
Browse code

geom_cladelabel now support `angle="auto"`

GuangchuangYu authored on 05/05/2017 21:01:50
Showing1 changed files
... ...
@@ -1,3 +1,7 @@
1
+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
 ------------------------
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
Showing1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 1.8.0
2
+------------------------
3
+ o BioC 3.5 release <2017-04-26, Wed>
4
+
1 5
 CHANGES IN VERSION 1.7.11
2 6
 ------------------------
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
Showing1 changed files
... ...
@@ -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>
Browse code

message for defunct functions

guangchuang yu authored on 23/03/2017 03:40:26
Showing1 changed files
... ...
@@ -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
Browse code

update subview

guangchuang yu authored on 13/03/2017 05:39:11
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
1 1
 CHANGES IN VERSION 1.7.9
2 2
 ------------------------
3
+ 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
Showing1 changed files
... ...
@@ -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>
Browse code

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

guangchuang yu authored on 01/03/2017 08:49:58
Showing1 changed files
... ...
@@ -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
Browse code

remove apeBootstrap and raxml object support as they were removed from treeio

guangchuang yu authored on 28/02/2017 07:11:57
Showing1 changed files
... ...
@@ -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>
Browse code

parse="emoji" :)

guangchuang yu authored on 16/02/2017 06:54:38
Showing1 changed files
... ...
@@ -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>
Browse code

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

guangchuang yu authored on 16/02/2017 06:10:17
Showing1 changed files
... ...
@@ -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>
Browse code

update docs

guangchuang yu authored on 13/02/2017 05:33:14
Showing1 changed files
... ...
@@ -1,5 +1,7 @@
1 1
 CHANGES IN VERSION 1.7.7
2 2
 ------------------------
3
+ 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
Browse code

update citation

GuangchuangYu authored on 20/01/2017 05:21:52
Showing1 changed files
... ...
@@ -1,3 +1,7 @@
1
+CHANGES IN VERSION 1.7.7
2
+------------------------
3
+ o update citation info <2017-01-20, Fri>
4
+ 
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
Showing1 changed files
... ...
@@ -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>
Browse code

not labeling collapsed clade as tip

guangchuang yu authored on 03/01/2017 03:47:16
Showing1 changed files
... ...
@@ -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>
Browse code

fortify.phylo4d via converting phylo4d to treedata object

guangchuang yu authored on 28/12/2016 13:49:47
Showing1 changed files
... ...
@@ -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
 
Browse code

better viewClade

guangchuang yu authored on 28/12/2016 08:08:07
Showing1 changed files
... ...
@@ -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>
Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
Showing1 changed files
... ...
@@ -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>
Browse code

is.ggtree

guangchuang yu authored on 06/12/2016 07:53:23
Showing1 changed files
... ...
@@ -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>
Browse code

branch.length support phylo4d@data

guangchuang yu authored on 06/12/2016 05:42:11
Showing1 changed files
... ...
@@ -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>
Browse code

bug fixed of rm.singleton.newick

guangchuang yu authored on 01/12/2016 04:40:01
Showing1 changed files
... ...
@@ -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
Browse code

postorder

guangchuang yu authored on 28/11/2016 05:42:43
Showing1 changed files
... ...
@@ -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>
Browse code

phylo4d

guangchuang yu authored on 24/11/2016 05:04:08
Showing1 changed files
... ...
@@ -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
 
Browse code

overlap parameter in groupOTU

guangchuang yu authored on 16/11/2016 05:54:24
Showing1 changed files
... ...
@@ -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>
Browse code

fixed drop.tip issues

guangchuang yu authored on 11/11/2016 05:33:47
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
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
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
1 1
 CHANGES IN VERSION 1.7.3
2 2
 ------------------------
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
 
guangchuang yu authored on 07/11/2016 03:16:33
Showing1 changed files
... ...
@@ -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>
Browse code

make missing color invisible

GuangchuangYu authored on 03/11/2016 15:30:13
Showing1 changed files
... ...
@@ -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>
Browse code

xlim_expand

guangchuang yu authored on 01/11/2016 02:38:09
Showing1 changed files
... ...
@@ -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
 
Browse code

expand_xlim

guangchuang yu authored on 01/11/2016 02:23:02
Showing1 changed files
... ...
@@ -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
Browse code

bug fixed of parsing treetext in beast file

guangchuang yu authored on 31/10/2016 11:29:54
Showing1 changed files
... ...
@@ -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>
Browse code

xlim_tree

guangchuang yu authored on 31/10/2016 07:41:12
Showing1 changed files
... ...
@@ -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
Browse code

set_tree_xlim

guangchuang yu authored on 31/10/2016 04:10:22
Showing1 changed files
... ...
@@ -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>
Browse code

facet_plot supports ggbio::geom_alignment

guangchuang yu authored on 26/10/2016 08:27:56
Showing1 changed files
... ...
@@ -1,5 +1,7 @@
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
Showing1 changed files
... ...
@@ -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>
Browse code

bioc 3.5

guangchuang yu authored on 18/10/2016 01:23:55
Showing1 changed files
... ...
@@ -1,3 +1,7 @@
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
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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
Browse code

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

guangchuang yu authored on 11/10/2016 06:41:22
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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>
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
Showing1 changed files
... ...
@@ -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
309 311
 ------------------------
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
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -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
Showing1 changed files
... ...
@@ -1,5 +1,6 @@
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
Showing1 changed files
... ...
@@ -1,5 +1,7 @@
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
Showing1 changed files