-
Notifications
You must be signed in to change notification settings - Fork 172
/
NEWS
783 lines (675 loc) · 36.4 KB
/
NEWS
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
CHANGES IN VERSION 1.11.3
------------------------
o update msaplot to use DNAbin/AAbin internally and also compatible with treedata object <2017-12-14, Thu>
o clean up code <2017-12-13, Thu>
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>
CHANGES IN VERSION 1.11.2
------------------------
o keep tree order (previously using postorder) <2017-12-06-Wed>
+ https://github.com/GuangchuangYu/ggtree/issues/157
o remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>
o deprecate subview, annotation_image and phylopic; remove theme_transparent <2017-12-04, Mon>
o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>
o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>
CHANGES IN VERSION 1.11.1
------------------------
o bug fixed in geom_tiplab, now `offset` parameter works with `align=TRUE`. <2017-11-20, Mon>
o enable mrsd parameter for treedata object <2017-11-15, Wed>
o set_hilight_legend supports alpha parameter <2017-11-15, Wed>
+ https://github.com/GuangchuangYu/ggtree/issues/149
CHANGES IN VERSION 1.9.4
------------------------
o geom_hilight_encircle and geom_cladelabel2 <2017-09-12, Tue>
+ https://github.com/GuangchuangYu/ggtree/pull/152
o set_hilight_legend <2017-08-30, Wed>
o geom_motif for aligned motif <2017-08-22, Tue>
+ https://github.com/GuangchuangYu/ggtree/issues/148
o fixed `R CMD build` error: cannot stat 'ggtree/site_src/themes': No such file or directory <2017-08-22, Tue>
CHANGES IN VERSION 1.9.3
------------------------
o update to using !! in tidyr::gather for compatible with tidyr 0.7.0 <2017-08-03, Thu>
o now geom_text2, geom_label2, geom_point2 and geom_segment2 work with ggplot2 <2017-08-01, Tue>
o update fortify.jplace to support number of placement (nplace) <2017-07-27, Thu>
CHANGES IN VERSION 1.9.2
------------------------
o add bg_line and height parameter in msaplot <2017-07-26, Wed>
+ use can set bg_line = FALSE and height = 1 to plot more beautiful alignment
o extend parameter in geom_cladebar <2017-07-26, Wed>
+ https://github.com/GuangchuangYu/ggtree/issues/142#issuecomment-317817995
o scaleClade works after calling viewClade <2017-07-20, Thu>
+ https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/QVSryszPaFY
o gheatmap support handling collapsed tree <2017-06-29, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/137
CHANGES IN VERSION 1.9.1
------------------------
o now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon>
o geom_cladelabel support `angle="auto"` for circular layout tree <2017-05-05, Fri>
CHANGES IN VERSION 1.8.0
------------------------
o BioC 3.5 release <2017-04-26, Wed>
CHANGES IN VERSION 1.7.11
------------------------
o remove layout.method parameter <2017-04-20, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/118#issuecomment-295130818
+ https://github.com/GuangchuangYu/ggtree/issues/125
CHANGES IN VERSION 1.7.10
------------------------
o add message for subview, inset, phylopic, theme_transparent and theme_inset <2017-03-23, Thu>
+ will be defunct in version >= 1.9.0
+ user should use ggimage package to annotate tree with graphic object or image file
o update subview to support mainview produced by `ggplot() + layers` <2017-03-13, Mon>
CHANGES IN VERSION 1.7.9
------------------------
o fixed geom_range to support height_0.95_HPD <2017-03-03, Fri>
o fixed geom_tiplab(geom='label') <2017-03-02, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/115
CHANGES IN VERSION 1.7.8
------------------------
o get_taxa_name now sorted by taxa position and also support whole tree <2017-03-01, Wed>
o unrooted layout support branch.length="none", fixed #114 <2017-03-01, Wed>
o remove apeBootstrap and raxml object support as they were removed from treeio <2017-02-28, Tue>
CHANGES IN VERSION 1.7.7
------------------------
o supports parse="emoji" in geom_cladelabel, geom_text2, geom_label2, geom_tiplab, geom_tiplab2 <2017-02-16, Thu>
o aes(subset) now support logical vector contains NA <2017-02-16, Thu>
o add legend transparency to theme_transparent <2017-02-13, Mon>
+ <https://github.com/GuangchuangYu/ggtree/pull/112>
o update citation info <2017-01-20, Fri>
CHANGES IN VERSION 1.7.6
------------------------
o inset support reverse scale <2017-01-05, Thu>
+ https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/_JPfm71Z8nM/6gL93oxHFQAJ
CHANGES IN VERSION 1.7.5
------------------------
o disable labeling collapsed node as tip <2017-01-03, Tue>
+ https://groups.google.com/forum/#!topic/bioc-ggtree/nReqJatMvJQ
o fortify.phylo4d via converting phylo4d to treedata object <2016-12-28, Wed>
o improve viewClade function, use coord_cartesian instead of xlim <2016-12-28, Wed>
o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
CHANGES IN VERSION 1.7.4
------------------------
o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue>
o now branch.length can set to feature available in phylo4d@data and yscale is supported for phylo4d object <2016-12-06, Tue>
o bug fixed of rm.singleton.newick, remove singleton parent instead of singleton <2016-12-01, Thu>
o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/98
o groupOTU method now accept 'overlap = c("overwrite", "origin", "abandon")' parameter <2016-11-16, Wed>
+ https://groups.google.com/forum/#!topic/bioc-ggtree/Q4LnwoTf1DM
CHANGES IN VERSION 1.7.3
------------------------
o drop.tip method for NHX object <2016-11-11, Fri>
o update startup message <2016-11-09, Wed>
o reverse timescale x-axis <2016-11-07, Mon>
+ https://github.com/GuangchuangYu/ggtree/issues/87
CHANGES IN VERSION 1.7.2
------------------------
o make missing colors in gheatmap invisible (previously use 'white') <2016-11-03, Thu>
o xlim_expand for setting x axis limits of specific panel <2016-11-01, Tue>
+ xlim_tree is now a specific case of xlim_expand(xlim, panel='Tree')
o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
+ https://github.com/GuangchuangYu/ggtree/issues/84
CHANGES IN VERSION 1.7.1
------------------------
o xlim_tree layer and test <2016-10-31, Mon>
+ set x axis limits for Tree panel for facet_plot
o update read.nhx <2016-10-30, Sun>
+ add tip numbers to @nhx_tags and add tests
+ https://github.com/GuangchuangYu/ggtree/pull/83
+ store nhx_tags$node as numeric values <2016-10-31, Mon>
o facet_plot supports ggbio::geom_alignment <2016-10-26, Wed>
+ https://github.com/tengfei/ggbio/issues/83
o make tree stats available in facet_plot <2016-10-24, Mon>
CHANGES IN VERSION 1.6.0
------------------------
o BioC 3.4 released <2016-10-18, Tue>
CHANGES IN VERSION 1.5.17
------------------------
o read.nhx support newick file <2016-10-17, Mon>
+ https://github.com/GuangchuangYu/ggtree/issues/79
CHANGES IN VERSION 1.5.16
------------------------
o read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue>
+ https://www.biostars.org/p/210401/#216128
o fixed aes mapping in geom_strip <2016-10-11, Tue>
o fixed R check <2016-10-10, Mon>
+ check.aes parameter is not available in release version of ggplot2 yet
CHANGES IN VERSION 1.5.15
------------------------
o check.aes for layers defined in ggtree <2016-10-07, Fri>
o recalculate 'angle' when collapse, expand and rotate clade <2016-10-06, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/78
CHANGES IN VERSION 1.5.14
------------------------
o subset tip in geom_tiplab2 <2016-10-05, Wed>
o add `compute_group` according to ggplot (v2.1.0) <2016-09-29, Thu>
+ https://github.com/hadley/ggplot2/issues/1797
o unit test for groupOTU and groupClade <2016-09-22, Thu>
o groupOTU label groups by input group names (when input is a named list) <2016-09-22, Thu>
o update angle calculation for geom_tiplab <2016-09-13, Thu>
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>
+ currently only phylo object supported.
+ add test for as.polytomy
CHANGES IN VERSION 1.5.13
------------------------
o facet_plot for plotting data with tree <2016-09-06, Tue>
o more parameters for column names in gheatmap <2016-09-06, Tue>
+ colnames_angle
+ colnames_offset_x
+ colnames_offset_y
+ hjust
o offset parameter in geom_tiplab and geom_tiplab2 <2016-09-05, Mon>
CHANGES IN VERSION 1.5.12
------------------------
o use data in all layers instead of the base layer for coordination calculation in subview <2016-09-01, Thu>
o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
CHANGES IN VERSION 1.5.11
------------------------
o gheatmap works with matrix <2016-08-28, Sun>
+ https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/2YLvXHMJJ6U/c4zS7yfGCAAJ
o support parsing expression in geom_strip <2016-08-18, Thu>
o bug fixed in geom_tiplab <2016-08-17, Wed>
+ https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ
o update citation info, add doi. <2016-08-16, Tue>
CHANGES IN VERSION 1.5.10
------------------------
o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
+ https://github.com/GuangchuangYu/ggtree/issues/72
CHANGES IN VERSION 1.5.9
------------------------
o update citation info <2016-08-12, Fri>
CHANGES IN VERSION 1.5.8
------------------------
o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu>
o geom_cladelabel support parsing expression <2016-08-11, Thu>
CHANGES IN VERSION 1.5.7
------------------------
o geom_strip can accept taxa name as input but labeling strip will not supported.
To support labeling strip, user need to input node id <2016-07-27, Wed>
o nodeid function for converting node label(s) to node id(s) <2016-07-27, Wed>
CHANGES IN VERSION 1.5.6
------------------------
o remove dependency of Biostring for installing ggtree <2016-07-21, Thu>
+ still needed for building vignette and for processing FASTA file
o remove dependency of EBImage for building & installing ggtree <2016-07-21, Thu>
+ the package is still needed if user want to annotate tree with image file
o `%<+%` now works with tbl_df <2016-07-21, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/66
o identify method for ggtree <2016-06-28, Tue>
+ see https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree
o geom_balance contributed by Justin Silverman <2016-06-22, Wed>
+ see https://github.com/GuangchuangYu/ggtree/pull/64
CHANGES IN VERSION 1.5.5
------------------------
o update geom_tiplab2 according to angle change introduced by open_tree <2016-06-20, Mon>
o bug fixed in collapse, now work with collapse a clade that contain a subclade that was already collapsed <2016-06-02-Thu>
o bug fixed if time-scaled tree extend into the BCE. <2016-06-02, Thu>
+ as.Date won't work for BCE time.
+ as.Date=FALSE by default in fortify method, just use the time in decimal format (real number, not Date object).
CHANGES IN VERSION 1.5.4
------------------------
o reroot method for raxml object <2016-05-22, Sun>
o bug fixed in scaleClade, now y positions are (hopefully) always correct. <2016-05-20, Fri>
o bug fixed in collapse <2016-05-20, Fri>
+ if user collapse a node that is an offspring of a collapsed node, print warning msg and return the tree directly
o use byte compiler <2016-05-18, Wed>
o change any(is.na()) to anyNA() which is more efficient <2016-05-18, Wed>
o https://github.com/Bioconductor-mirror/ggtree/commit/559548c66b51253e8ccb983d353385838a81f106
CHANGES IN VERSION 1.5.3
------------------------
o add examples in vignettes <2016-05-13, Fri>
+ add fan layout example in treeVisualization vignette
+ add open_tree and rotate_tree example in treeManipulation vignette
o add angle in ggtree function, fan layout supported <2016-05-12, Thu>
o rotate_tree and open_tree function <2016-05-12, Thu>
o support reading BEAST MCC trees (multiple trees in one file) via the read.beast function <2016-05-12, Thu>
o https://github.com/Bioconductor-mirror/ggtree/commit/51eec4721595c274c24dc4df2f1fdf40700cb1a5
CHANGES IN VERSION 1.5.2
------------------------
o add multiplot in ggtreeUtilities vignette <2016-05-12, Thu>
o add example of integrate user's data using phylo4d in treeAnnotation vignette <2016-05-11, Wed>
o add extend, extendto parameter in geom_hilight <2016-05-10, Tue>
o geom_hilight now supports hilight tips <2016-05-10, Tue>
+ https://github.com/GuangchuangYu/ggtree/issues/53
o more accurate ylim & angle for circular layout <2016-05-10, Tue>
+ https://github.com/GuangchuangYu/ggtree/issues/40
o supports phylo4d object <2016-05-10, Tue>
+ https://github.com/GuangchuangYu/ggtree/issues/47
CHANGES IN VERSION 1.5.1
------------------------
o update vignettes <2016-05-10, Tue>
+ add geom_range example in treeImport
+ add geom_strip and geom_taxalink example in treeAnnotation
+ add ggtreeUtilities vignette
o gheatmap now works with data.frame of only one column <2016-05-09, Mon>
+ contributed by Justin Silverman <[email protected]>
+ https://github.com/GuangchuangYu/ggtree/pull/57
o geom_strip for associated taxa <2016-05-09, Mon>
+ https://github.com/GuangchuangYu/ggtree/issues/52
CHANGES IN VERSION 1.4.0
------------------------
o BioC 3.3 released <2016-05-05, Thu>
CHANGES IN VERSION 1.3.16
------------------------
o geom_treescale() supports family argument <2016-04-27, Wed>
+ https://github.com/GuangchuangYu/ggtree/issues/56
o update fortify.phylo to work with phylo that has missing value of edge length <2016-04-21, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/54
o support passing textConnection(text_string) as a file <2016-04-21, Thu>
+ contributed by Casey Dunn <[email protected]>
+ https://github.com/GuangchuangYu/ggtree/pull/55#issuecomment-212859693
CHANGES IN VERSION 1.3.15
------------------------
o geom_tiplab2 supports parameter hjust <2016-04-18, Mon>
o geom_tiplab and geom_tiplab2 support using geom_label2 by passing geom="label" <2016-04-07, Thu>
o geom_label2 that support subsetting <2016-04-07, Thu>
o geom_tiplab2 for adding tip label of circular layout <2016-04-06, Wed>
o use plot$plot_env to access ggplot2 parameter <2016-04-06, Wed>
o geom_taxalink for connecting related taxa <2016-04-01, Fri>
o geom_range for adding range of HPD to present uncertainty of evolutionary inference <2016-04-01, Fri>
CHANGES IN VERSION 1.3.14
------------------------
o geom_tiplab works with NA values, compatible with collapse <2016-03-05, Sat>
o update theme_tree2 due to the issue of https://github.com/hadley/ggplot2/issues/1567 <2016-03-05, Sat>
o offset works in `align=FFALSE` with `annotation_image` function <2016-02-23, Tue>
+ see https://github.com/GuangchuangYu/ggtree/issues/46
o subview and inset now supports annotating with img files <2016-02-23, Tue>
CHANGES IN VERSION 1.3.13
------------------------
o add example of rescale_tree function in treeAnnotation.Rmd <2016-02-07, Sun>
o geom_cladelabel works with collapse <2016-02-07, Sun>
+ see https://github.com/GuangchuangYu/ggtree/issues/38
CHANGES IN VERSION 1.3.12
------------------------
o exchange function name of geom_tree and geom_tree2 <2016-01-25, Mon>
o solved issues of geom_tree2 <2016-01-25, Mon>
+ https://github.com/hadley/ggplot2/issues/1512
o colnames_level parameter in gheatmap <2016-01-25, Mon>
o raxml2nwk function for converting raxml bootstrap tree to newick format <2016-01-25, Mon>
CHANGES IN VERSION 1.3.11
------------------------
o solved issues of geom_tree2 <2016-01-25, Mon>
+ https://github.com/GuangchuangYu/ggtree/issues/36
o change compute_group() to compute_panel in geom_tree2() <2016-01-21, Thu>
+ fixed issue, https://github.com/GuangchuangYu/ggtree/issues/36
o support phyloseq object <2016-01-21, Thu>
o update geom_point2, geom_text2 and geom_segment2 to support setup_tree_data <2016-01-21, Thu>
o implement geom_tree2 layer that support duplicated node records via the setup_tree_data function <2016-01-21, Thu>
o rescale_tree function for rescaling branch length of tree object <2016-01-20, Wed>
o upgrade set_branch_length, now branch can be rescaled using feature in extraInfo slot <2016-01-20, Wed>
CHANGES IN VERSION 1.3.10
------------------------
o remove dependency of gridExtra by implementing multiplot function instead of using grid.arrange <2016-01-20, Wed>
o remove dependency of colorspace <2016-01-20, Wed>
o support phylip tree format and update vignette of phylip example <2016-01-15, Fri>
CHANGES IN VERSION 1.3.9
------------------------
o optimize getYcoord <2016-01-14, Thu>
o add 'multiPhylo' example in 'Tree Visualization' vignette <2016-01-13, Wed>
o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.
these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>
+ > ggtree(rtree(30)); viewClade(node=35) works. no need to pipe.
CHANGES IN VERSION 1.3.8
------------------------
o add example of viewClade in 'Tree Manipulation' vignette <2016-01-13, Wed>
o add viewClade function <2016-01-12, Tue>
o support obkData object defined by OutbreakTools <2016-01-12, Tue>
o update vignettes <2016-01-07, Thu>
o 05 advance tree annotation vignette <2016-01-04, Mon>
o export theme_inset <2016-01-04, Mon>
o inset, nodebar, nodepie functions <2015-12-31, Thu>
CHANGES IN VERSION 1.3.7
------------------------
o split the long vignette to several vignettes
+ 00 ggtree <2015-12-29, Tue>
+ 01 tree data import <2015-12-28, Mon>
+ 02 tree visualization <2015-12-28, Mon>
+ 03 tree manipulation <2015-12-28, Mon>
+ 04 tree annotation <2015-12-29, Tue>
CHANGES IN VERSION 1.3.6
------------------------
o MRCA function for finding Most Recent Common Ancestor among a vector of tips <2015-12-22, Tue>
o geom_cladelabel: add bar and label to annotate a clade <2015-12-21, Mon>
- remove annotation_clade and annotation_clade2 functions.
o geom_treescale: tree scale layer. (add_legend was removed) <2015-12-21, Mon>
CHANGES IN VERSION 1.3.5
------------------------
o bug fixed, read.nhx now works with scientific notation <2015-11-30, Mon>
+ see https://github.com/GuangchuangYu/ggtree/issues/30
CHANGES IN VERSION 1.3.4
------------------------
o rename beast feature when name conflict with reserve keywords (label, branch, etc) <2015-11-27, Fri>
o get_clade_position function <2015-11-26, Thu>
+ https://github.com/GuangchuangYu/ggtree/issues/28
o get_heatmap_column_position function <2015-11-25, Wed>
+ see https://github.com/GuangchuangYu/ggtree/issues/26
o support NHX (New Hampshire X) format via read.nhx function <2015-11-17, Tue>
o bug fixed in extract.treeinfo.jplace <2015-11-17, Thu>
CHANGES IN VERSION 1.3.3
------------------------
o support color=NULL in gheatmap, then no colored line will draw within the heatmap <2015-10-30, Fri>
o add `angle` for also rectangular, so that it will be available for layout='rectangular' following by coord_polar() <2015-10-27, Tue>
CHANGES IN VERSION 1.3.2
------------------------
o update vignette, add example of ape bootstrap and phangorn ancestral sequences <2015-10-26, Mon>
o add support of ape bootstrap analysis <2015-10-26, Mon>
see https://github.com/GuangchuangYu/ggtree/issues/20
o add support of ancestral sequences inferred by phangorn <2015-10-26, Mon>
see https://github.com/GuangchuangYu/ggtree/issues/21
CHANGES IN VERSION 1.3.1
------------------------
o change angle to angle + 90, so that label will in radial direction <2015-10-22, Thu>
+ see https://github.com/GuangchuangYu/ggtree/issues/17
o na.rm should be always passed to layer(), fixed it in geom_hilight and geom_text2 <2015-10-21, Wed>
+ see https://github.com/hadley/ggplot2/issues/1380
o matching beast stats with tree using internal node number instead of label <2015-10-20, Tue>
CHANGES IN VERSION 1.2.0
------------------------
o BioC 3.2 released
CHANGES IN VERSION 1.1.21
------------------------
o support hyphy output of ancestral sequences that is in phylip sequential format (no TAXALABELS block available) <2015-10-07, Wed>
o fixed bug in geom_tiplab when x contains NA (eg, removing by collapse function) <2015-10-01, Thu>
o new implementation of geom_hilight, a truly geom layer function <2015-09-10, Thu>
CHANGES IN VERSION 1.1.20
------------------------
o bug fixed in %add2%, if node available use node, otherwise use label <2015-09-04, Fri>
o bug fixed of subview for considering aes mapping of x and y <2015-09-03, Thu>
o update vignette by adding r8s example <2015-09-02, Wed>
o defined r8s class, see http://loco.biosci.arizona.edu/r8s/ <2015-09-02, Wed>
+ add r8s sample files
+ read.r8s, parser function
+ fortify method
+ plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
o bug fixed in fortify.multiPhylo, convert df$.id to factor of levels=names(multiPhylo_object) <2015-09-02, Wed>
o update scale_x_ggtree to support Date as x-axis <2015-09-01, Tue>
o add mrsd parameter for user to specify 'most recent sampling date' for time tree <2015-09-01, Tue>
- remove 'time_scale' parameter.
o defined 'raxml' class for RAxML bootstrapping analysis result <2015-09-01, Tue>
+ see http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html
+ read.raxml, parser function
+ plot, get.tree, get.fields, groupOTU, groupClade, scale_color, gzoom and show methods
+ fortify.raxml method
o bug fixed in edgeNum2nodeNum for jplace parsing jplace file <2015-09-01, Tue>
CHANGES IN VERSION 1.1.19
------------------------
o use fortify instead of fortify.phylo in fortify.multiPhylo,
so that multiPhylo can be a list of beast/codeml or other supported objects. <2015-08-31, Mon>
o support multiPhylo object, should use + facet_wrap or + facet_grid <2015-08-31, Mon>
o remove dependency of EBImage and phytools to speedup the installation process of ggtree <2015-08-31, Mon>
+ these two packages is not commonly used, and will be loaded automatically when needed.
CHANGES IN VERSION 1.1.18
------------------------
o layout name change to 'rectangular', 'slanted', 'circular'/'fan' for phylogram and cladogram (if branch.length = 'none')
'unroot' is not changed. <2015-08-28. Fri>
o implement geom_point2, geom_text2, geom_segment2 to support subsetting <2015-08-28, Fri>
see https://github.com/hadley/ggplot2/issues/1295
o update geom_tiplab according to geom_text2 and geom_segment2 <2015-08-28, Fri>
o add geom_tippoint, geom_nodepoint and geom_rootpoint <2015-08-28, Fri>
CHANGES IN VERSION 1.1.17
------------------------
o bug fixed in rm.singleton.newick by adding support of scientific notation in branch length <2015-08-27, Thu>
o bug fixed in gheatmap, remove inherit aes from ggtree <2015-08-27, Thu>
o add 'width' parameter to add_legend, now user can specify the width of legend bar <2015-08-27, Thu>
o add 'colnames_position' parameter to gheatmap, now colnames can be display on the top of heatmap <2015-08-27, Thu>
o theme_transparent to make background transparent <2015-08-27, Thu>
o subview for adding ggplot object (subview) to another ggplot object (mainview) <2015-08-27, Thu>
CHANGES IN VERSION 1.1.16
------------------------
o update citation <2015-08-17, Mon>
CHANGES IN VERSION 1.1.15
------------------------
o open text angle parameter for annotation_clade/annotation_clade2 <2015-08-13, Thu>
o support changing size of add_legend <2015-08-13, Thu>
o reroot methods for phylo and beast <2015-08-07, Fri>
CHANGES IN VERSION 1.1.14
------------------------
o update paml_rst to compatible with only marginal ancestral sequence or joint ancestral sequence available <2015-08-07, Fri>
CHANGES IN VERSION 1.1.13
------------------------
o implement annotation_image <2015-08-01, Sat>
o better implementation of geom_tiplab for accepting aes mapping and auto add align dotted line <2015-08-01, Sat>
o open group_name parameter of groupOTU/groupClade to user <2015-08-01, Sat>
CHANGES IN VERSION 1.1.12
------------------------
o update vignette according to the changes <2015-07-31, Fri>
o add mapping parameter in ggtree function <2015-07-31, Fri>
o extend groupClade to support operating on tree view <2015-07-31, Fri>
o extend groupOTU to support operating on tree view <2015-07-31, Fri>
o new implementation of groupClade & groupOTU <2015-07-31, Fri>
CHANGES IN VERSION 1.1.11
------------------------
o annotation_clade and annotation_clade2 functions. <2015-07-30, Thu>
o better add_legend implementation. <2015-07-30, Thu>
o add ... in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu>
o better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu>
CHANGES IN VERSION 1.1.10
------------------------
o solve overlapping branches for layout = "fan" || "radial",
that are coord_polar-ized layouts.
see https://github.com/GuangchuangYu/ggtree/issues/6,
contributed by Vincent Bonhomme. <2015-07-22, Wed>
CHANGES IN VERSION 1.1.9
------------------------
o update add_legend to align legend text <2015-07-06, Mon>
o bug fixed in internal function, getChild.df, which should not include root node if selected node is root <2015-07-01, Wed>
o rotate function for ratating a clade by 180 degree and update vignette <2015-07-01, Wed>
o get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue>
o add example of flip function in vignette <2015-06-30, Tue>
o flip function for exchanging positions of two selected branches <2015-06-30, Tue>
CHANGES IN VERSION 1.1.8
------------------------
o update get.placement <2015-06-05, Fri>
o edgeNum2nodeNum for converting edge number to node number for EPA/pplacer output <2015-06-04, Thu>
o mv scale_x_gheatmap to scale_x_ggtree, which also support msaplot <2015-06-02, Tue>
o add mask function <2015-06-02, Tue>
CHANGES IN VERSION 1.1.7
------------------------
o add example of msaplot in vignette <2015-05-22, Fri>
o msaplot for adding multiple sequence alignment <2015-05-22, Fri>
CHANGES IN VERSION 1.1.6
------------------------
o add vertical_only parameter to scaleClade and set to TRUE by default.
only vertical will be scaled by default. <2015-05-22, Fri>
o update add_colorbar & add_legend <2015-05-21, Thu>
o add example of add_legend and gheatmap in vignette <2015-05-18, Mon>
o gheatmap implementation of gplot <2015-05-18, Mon>
o add_legend for adding evolution distance legend <2015-05-18, Mon>
CHANGES IN VERSION 1.1.5
------------------------
o implement scaleClade <2015-05-12, Tue>
CHANGES IN VERSION 1.1.4
------------------------
o better performance of parsing beast tree <2015-05-11, Mon>
+ support beast tree begin with 'tree tree_1 = ' and other forms.
+ support file that only contains one evidence for some of the nodes/tips
o update add_colorbar to auto determine the position <2015-05-04, Mon>
o add_colorbar function <2015-04-30, Thu>
CHANGES IN VERSION 1.1.3
------------------------
o add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu>
o remove slash line in heatmap legend <2015-04-30, Thu>
o update vignette to add example of merge_tree <2015-04-29, Wed>
CHANGES IN VERSION 1.1.2
------------------------
o in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]* <2015-04-29, Wed>
o add examples folder in inst that contains sample data <2015-04-29, Wed>
o update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
o add line break if substitution longer than 50 character <2015-04-28, Tue>
o support calculating branch for time scale tree <2015-04-28, Tue>
o remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>
o scale_color accepts user specific interval and output contains 'scale' attribute that can be used for adding legend <2015-04-28, Tue>
o extend fortify methods to support additional fields <2015-04-28, Tue>
o extend get.fields methods to support additional fields <2015-04-28, Tue>
o extend tree class to support additional info by merging two tree <2015-04-28, Tue>
o implement merge_tree function to merge two tree objects into one <2015-04-28, Tue>
CHANGES IN VERSION 1.1.1
------------------------
o minor bug fixed in extracting node ID of rst file <2015-04-27, Mon>
o update parsing beast time scale tree to support _year (originally supports _year.\\d+) <2015-04-27, Mon>
o add Tommy in author <2015-04-27, Mon>
CHANGES IN VERSION 0.99.28
------------------------
o update vignette with floating table of content <2015-04-08, Wed>
CHANGES IN VERSION 0.99.27
------------------------
o bug fixed, see https://github.com/GuangchuangYu/ggtree/issues/4 <2015-03-07, Tue>
CHANGES IN VERSION 0.99.26
------------------------
o update geom_tiplab <2015-03-31, Tue>
o update plot method of beast <2015-03-17, Tue>
CHANGES IN VERSION 0.99.25
------------------------
o implement groupClade <2015-03-13, Fri>
CHANGES IN VERSION 0.99.24
------------------------
o use "round" segment end, look very better <2015-03-12, Thu>
o update vignett <2015-03-11, Wed>
CHANGES IN VERSION 0.99.23
------------------------
o mv geom_hilight to hilight <2015-03-11, Wed>
o mv geom_phylopic to phylopic <2015-03-11, Wed>
o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed>
CHANGES IN VERSION 0.99.22
------------------------
o remove quote in beast tip/node labels <2015-03-10, Tue>
CHANGES IN VERSION 0.99.21
------------------------
o fixed downloading png file in Windows platform, should explicitly setting mode="wb". <2015-03-03, Tue>
CHANGES IN VERSION 0.99.19
------------------------
o for time scale tree inferred by BEAST, now user can use time_scale=TRUE parameter in ggtree function <2015-02-12, Thu>
CHANGES IN VERSION 0.99.18
------------------------
o bug fixed in reorder the labels in gplot.heatmap <2015-02-12, Thu>
CHANGES IN VERSION 0.99.17
------------------------
o add angle and branch.y variable in cladogram layout <2015-02-10, Tue>
CHANGES IN VERSION 0.99.16
------------------------
o correct typo in vignette <2015-02-10, Tue>
CHANGES IN VERSION 0.99.15
------------------------
o fully support of replace operator, %<% <2015-02-09, Mon>
CHANGES IN VERSION 0.99.14
------------------------
o add example in groupOTU for adding legend manually <2015-02-09, Mon>.
CHANGES IN VERSION 0.99.13
------------------------
o two dimensional tree <2015-02-06, Fri>
CHANGES IN VERSION 0.99.12
------------------------
o update vignette <2015-02-04, Wed>
o gzoom methods that supports all tree objects <2015-02-04, Wed>
o geom_hilight layer for highlighting clade <2015-02-04, Wed>
CHANGES IN VERSION 0.99.11
------------------------
o add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed>
o revised groupOTU that output index can be used in geom_text and update vignette <2015-02-04, Wed>
CHANGES IN VERSION 0.99.10
------------------------
o support y scale by category variable <2015-02-03, Tue>
o support order nodes by yscale <2015-02-03, Tue>
CHANGES IN VERSION 0.99.9
------------------------
o update vignette <2015-02-02, Mon>
CHANGES IN VERSION 0.99.8
------------------------
o add get.phylopic function to read the online phylo pic and convert it to grob object,
which can be use to annotate ggplot figure using annotation_custom <2015-01-30, Fri>
CHANGES IN VERSION 0.99.7
------------------------
o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu>
CHANGES IN VERSION 0.99.6
------------------------
o read.beast now supports support values of sets such as {x, y, z} <2015-01-19, Mon>
o now read.beast supports characters in support values <2015-01-18, Sun>
o add example of gzoom and groupOTU in vignette <2015-01-14, Wed>
o implement groupOTU methods <2015-01-14, Wed>
o export get.offspring.tip <2015-01-14, Wed>
CHANGES IN VERSION 0.99.5
------------------------
o move ape and ggplot2 from Depends to Imports <2015-01-12, Mon>
o get.tipseq method for paml_rst and codeml object <2015-01-08, Thu>
o add gzoom function, similar to zoom function in ape <2015-01-07, Wed>
o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>
o remove <<- and update vignette <2015-01-06, Tue>
o update vignette and use BibTex and CSL for references <2015-01-05, Mon>
o update cladogram layout <2015-01-05, Mon>
o read.baseml function and update vignette with baseml example <2015-01-04, Sun>
o plot method for hyphy and hyphy example in vignette <2015-01-04, Sun>
o merge all vignettes to ggtree vignette <2015-01-04, Sun>
CHANGES IN VERSION 0.99.4
------------------------
o ggtree now support branch.length = "none" to only draw tree topology <2015-01-03, Sat>
o get.subs method for hyphy object <2015-01-03, Sat>
o show, get.tree and get.subs methods of hyphy <2015-01-02, Fri>
o export read.hyphy <2015-01-02, Fri>
o export hyphy class <2015-01-01, Thu>
o plot method for beast class and get.tree method for codeml class <2014-12-31, Wed>
o show, get.fields, get.subs and plot methods for codeml class <2014-12-30, Tue>
o plot method for paml_rst class <2014-12-30, Tue>
o get.subs, method for paml_rst class <2014-12-30, Tue>
o show, plot, get.tree and fority methods for codeml_mlc class <2014-12-29, Mon>
o codeml class <2014-12-29, Mon>
o hyphy class and read.hyphy prototype <2014-12-27, Sat>
o update man file and add example file of beast output <2014-12-26, Fri>
o get.tree and get.fileds methods of beast class <2014-12-26, Fri>
o read.beast <2014-12-26, Fri>
o beast class and show method <2014-12-26, Fri>
o coplot prototype<2014-12-24, Wed>
o parse translation matrix in beast nexus <2014-12-24, Wed>
o extract beast stats info <2014-12-23, Tue>
CHANGES IN VERSION 0.99.3
------------------------
o gplot function that can view a tree and an associated matrix simultaneously <2014-12-22, Mon>
o modified vignette to show based on branch position and break the evolution distance scale <2014-12-22, Mon>
o label and annotation can be put based on branch. <2014-12-22, Mon>
o write.jplace and fully supports of jplace by ggtree. <2014-12-21, Sun>
o support unrooted layout in ggplot. <2014-12-21, Sun>
o support fan, radial, dendrogram layout in geom_tree. <2014-12-21, Sun>
CHANGES IN VERSION 0.99.2
------------------------
o layout of unrooted tree, implemented equal-angle algorithm that described in Chapter 34
of 'Inferring Phylogenies' (page 578-580) <2014-12-20, Sat>
o add layout parameter in ggtree and geom_tree, now supports phylogram and cladogram <2014-12-20, Sat>
o %<+% function for inserting annotation data to a tree view <2014-12-20, Sat>
o update ggtree-treeAnnotation vignette <2014-12-20, Sat>
CHANGES IN VERSION 0.99.1
------------------------
o %<% function for updating tree view with a new tree <2014-12-19, Fri>
o add examples in man files <2014-12-19, Fri>
CHANGES IN VERSION 0.2.3
------------------------
o add README.md <2014-12-19, Fri>
o update ggtree-treeViewer vignette <2014-12-19, Fri>
o use BiocStyle in vignette <2014-12-19, Fri>
o geom_nplace and geom_place layer <2014-12-18, Thu>
o add theme_tree2 theme for showing evolution distance <2014-12-18, Thu>
o rm.singleton.newick now supports internal node like:
((()X, ()Y)Z)AA, in which Z is a singleton. <2014-12-15, Mon>
CHANGES IN VERSION 0.2.2
------------------------
o rm.singleton.newick <2014-12-09, Tue>
o as.binary method <2014-12-09, Tue>
CHANGES IN VERSION 0.2.1
------------------------
o geom_eplace <2014-12-07, Sun>
CHANGES IN VERSION 0.2.0
------------------------
o read.jplace to read the jplace file <2014-12-05, Fri>
o jplace class for storing information of jplace file <2014-12-05, Fri>
o show method of jplace class <2014-12-05, Fri>
o get.tree method to get tree from jplace class <2014-12-05, Fri>
o extend ggplot2 to support jplace class <2014-12-05, Fri>
CHANGES IN VERSION 0.1.1
------------------------
o add distance legend in ggtree <2014-12-05, Fri>
CHANGES IN VERSION 0.1.0
------------------------
o support ladderize tree <2014-12-05, Fri>
o implement geom_tree, geom_tiplab, geom_tippoint, geom_aline and theme_tree <2014-12-04, Thu>
o extend ggplot to support phylo object and implement ggtree function <2014-12-04, Thu>
o implement fortify function <2014-12-04, Thu>
o add getRoot, isRoot and getParent functions <2014-12-03, Wed>