NEWS.md
db6d5e27
 # ggtree 2.1.1
 
 + fixed `fontface` warning message when `align=TRUE` in `geom_tiplab` (2019-10-30, Wed)
   - <https://github.com/YuLab-SMU/ggtree/issues/260>
 
 # ggtree 2.0.0
 
 + Bioconductor 3.10 release (2019-10-30, Wed)
 
87cb27be
 # ggtree 1.99.1
 
e8f6f87a
 + bug fixed of `geom_hilight` for `tree$edge.length = NULL` (2019-10-16, Wed)
   - <https://groups.google.com/d/msg/bioc-ggtree/GULj-eoAluI/Llpm-HbfCwAJ>
81382246
 + `fortify` method for igraph (only work with tree graph) (2019-09-28, Sat)
87cb27be
 + `ggdensitree` (2019-09-11, Wed)
   - <https://github.com/YuLab-SMU/ggtree/pull/253>
61b9be0f
   - <https://github.com/YuLab-SMU/ggtree/pull/255> 
   - <https://yulab-smu.github.io/treedata-book/chapter4.html#visualize-a-list-of-trees>
 
eb32147b
 # ggtree 1.99.0
 
 + prepare for ggtree v=2.0.0
 
cee2cc25
 # ggtree 1.17.5
 
dce1205a
 + `fortify` methods for hierarchical clustering objects, including `agnes`, `diana` and `twins` (2019-08-30, Fri) 
f31fbd75
 + now `geom_hilight` supports `unrooted` and `daylight` layouts (2019-08-28, Wed)
61b9be0f
   - by calling `geom_hilight_encircle`
2c14b064
 + update `geom_motif` according to the change of `gggenes` and allow labeling genes (2019-08-27, Tue)
   - <https://yulab-smu.github.io/treedata-book/chapter11.html#genome-locus>
ea8ffdd5
 + re-implement `geom_strip` with more robust support of labelling strip, either input taxa using name or id.
cee2cc25
 + support `phylog` defined in ade4 package (2019-08-14, Wed)
2f52fc6b
   - <https://yulab-smu.github.io/treedata-book/chapter9.html#phylog>
ee07f0c3
 
0956944e
 # ggtree 1.17.4
 
aff471e1
 + now `geom_cladelabel` supports `unrooted` and `daylight` layouts (2019-08-14, Wed)
   - by integrating `geom_cladelabel2`
5a652171
 + defined `nodelab` method for ggtree to convert node number to label (2019-08-09, Fir)
 + redefined `nodeid` as S3 generic in `tidytree` v=0.2.6 
   - change the original function as a method for ggtree
   - move the `nodeid` function for tree object to treeio
222e9fd6
 + defunct `gzoom` function
 + introduce `rootnode` parameter in `geom_tree` with default = TRUE and behave as previous version (2019-08-08, Thu)
4f72df86
   - the invisible root to itself line segment have advantage for the number of line segments is consistent with the number of nodes. 
222e9fd6
   - if `rootnode = FALSE`, there will be no line segment of root to itself.
fd3b93fe
 + extend `gheatmap` to support collapsed node (2019-08-06, Tue)
   - <https://github.com/GuangchuangYu/ggtree/pull/243>
0956944e
 + support `hclust` and `dendrogram` (2019-07-31, Wed)
 
1418c053
 # ggtree 1.17.3
 
d3057fa1
 + remove re-export treeio parser function, user now need to load treeio explictly (2019-07-24, Wed) 
 + export `layout_circular`, `layout_fan` and `layout_rectangular`
 + `layout_dendrogram` and `theme_dendrogram` 
   - <https://yulab-smu.github.io/treedata-book/chapter10.html#dendrogram>
1418c053
 + `scale_x_range` for adding second x-axis for `geom_range` (2019-07-23, Tue)
 + change `branch.length` parameter to `center` for `geom_range`
 
6661d84b
 # ggtree 1.17.2
 
e6dc6e38
 + extend `expand` according to the change of `collapse` (2019-07-11, Thu)
 + `mode` parameter in `collapse`
585c3bd9
 + `geom_tiplab` now works with 'circular' and 'fan' layouts (2019-07-05, Fri)
b2d1f675
 + `geom_inset` for adding subplots to specific nodes (see also the `inset` function introduced in v=1.3.8)
6661d84b
 
c00aac1c
 # ggtree 1.17.1
 
4ef142fd
 + `facet_data` to extract data used in `facet_plot` or `geom_facet` (2019-07-02, Tue)
eeac7735
 + `continuous` parameter in `geom_tree` to to continuous color edge from parent to child (2019-09-25, Tue)
   - <https://yulab-smu.github.io/treedata-book/chapter4.html#color-tree>
98a43cd2
 + `root.position` parameter for `fortify` and `ggtree` (2019-05-27, Mon)
0d658ee7
 + `geom_facet`, a geom layer version of `facet_plot` (2019-05-23, Thu)
e5c982fb
 + update `scale_x_ggtree`, now we can use `gheatmap() + scale_x_ggtree()` (2019-05-22, Wed)
cc140056
 + extend `xlim_expand` to work with `ggplot2` (2019-05-20, Tue)
   - <https://yulab-smu.github.io/treedata-book/chapter9.html#xlim_expand>
c00aac1c
 + add `legend_title` variable in `gheatmap` (2019-05-16, Thu)
 
 # ggtree 1.16.0
 
 + Bioconductor 3.9 release
 
4c9fb8bb
 # ggtree 1.15.6
 
21dc5c83
 + compatible with range is NULL in `geom_range` (2019-04-27, Sat)
   - <https://groups.google.com/d/msg/bioc-ggtree/yNzjtioVVGU/MCh3MPl_CwAJ>
a0450f48
 + remove `getChild`, `getChild.df`, `getParent`, `getParent.df`, `getSibling`, `getAncestor` and `getAncestor.df`,
   instead use `child`, `parent`, `sibling` and `ancestor` methods implemented in `tidytree` and `treeio` (2019-01-30, Wed)
1dd645ce
 + remove `get.offspring.df` and `get.offspring.tip` and instead use `tidytree::offspring` (2019-01-28, Mon)
4c9fb8bb
 + `facet_widths` function to set relative widths of facet panels (2019-01-28, Mon)
   - the output is `ggplotify::as.ggplot(grid_object)`, so it is not the original `ggtree` object.
 
a0cd85ce
 # ggtree 1.15.5
 
2b9d5e9d
 + bug fixed of `theme_tree2` (2019-01-14, Mon)
   - <https://github.com/GuangchuangYu/ggtree/issues/218>  
a0cd85ce
 + mv `rescale_tree` to `treeio` (2019-01-11, Fri)
 
b6760093
 # ggtree 1.15.4
 
 + reimplement `MRCA` as a method inherited from `tidytree` (2019-01-10, Thu)
 + mv vignettes to [treedata-book](https://yulab-smu.github.io/treedata-book/) 
 
b7f2b5a1
 # ggtree 1.15.3
 
e45b2f26
 + move `reroot` method to `treeio` package and rename to `root` (2018-12-28, Fri)
b7f2b5a1
 + bug fixed for setting `branch.length="none"` in unrooted layouts (2018-12-26, Wed)
   - bug introduced in <https://github.com/GuangchuangYu/ggtree/pull/201>
 
21cbdbae
 # ggtree 1.15.2
 
 + compatible with `tibble` v=2.0.0 (2018-11-29, Thu)
 
c8bacdb1
 # ggtree 1.15.1
 
3d027bb4
 + now `revts` also reverse the `branch` column (2018-11-11, Sun)
   - <https://groups.google.com/d/msgid/bioc-ggtree/50765a34-53e5-44d2-bb8f-6d20a11fa890%40googlegroups.com>
c8bacdb1
 + better msg when taxa name not consistent in sequence and tree files with `msaplot`. (2018-11-07, Wed)
   - <https://github.com/GuangchuangYu/ggtree/issues/172#issuecomment-436585370>
   
 # ggtree 1.14.0
 
 + Bioconductor 3.8 release
 
b91f9a97
 # ggtree 1.13.6
 
919f823e
 + set `scale_y_continuous(expand = c(0, 0))` for `gheatmap` when `colnames = FALSE` (2018-10-17, Wed)
   - <https://github.com/GuangchuangYu/ggtree/issues/204>
b91f9a97
 + made data usable with treedata in 'equal_angle' and 'daylight' layouts (2018-10-11, Thu)
   - <https://github.com/GuangchuangYu/ggtree/pull/201>
   
e84c1f7e
 # ggtree 1.13.5
2c3a0a96
 
da41bd9e
 + enable additional parameters passed to `geom_rootedge` (2018-09-13, Thu)
   - <https://github.com/GuangchuangYu/ggtree/issues/195>
2c3a0a96
 + `facet_labeller` to label panels of `facet_plot` output (2018-09-10, Mon)
   - <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/nAl3bNswxQM/crBwKtS3BAAJ>
   
c3727414
 # ggtree 1.13.3
 
 + update `viewClade` according to the change of `ggplot2` (2018-08-07, Tue)
   - <https://github.com/GuangchuangYu/ggtree/issues/188>
   
6cd5161c
 # ggtree 1.13.2
4ec55777
 
38dda350
 + xmax_adjust  in `viewClade` (2018-07-21, Sat)
   - <https://github.com/GuangchuangYu/ggtree/issues/187>
6cd5161c
 + update rd of `facet_plot` by adding description and example (2018-07-19, Thu)
fb020874
 + order by y in `facet_plot` (2018-07-09, Mon)
41c82a6c
 + `extend` parameter in `geom_cladelabel` and `geom_strip` supports specifying
   extension of both sides (2018-07-06, Fri)
0d475eee
 + `geom_nodelab2` for circular layout (2018-07-03, Tue)
   - <https://groups.google.com/d/msgid/bioc-ggtree/cbe5e1e3-99c4-481d-8523-d5b50cf0460b%40googlegroups.com>
4ec55777
 + re-export `ggplot2::fortify`
   - <https://groups.google.com/d/msgid/bioc-ggtree/bf7a9b3c-9a8f-4d8d-a782-1b467fba38bc%40googlegroups.com>
 
4995cf2a
 # ggtree 1.13.1
50b227f1
 
5ae49127
 + `geom_nodepoint` & `geom_tippoint` now compatible with `ggplot2` v 2.2.1 &
4995cf2a
   3.0.0 (2018-06-26, Tue)
445bdce3
 + `geom_rootedge` (2018-06-13, Wed)
   - <https://github.com/GuangchuangYu/ggtree/issues/183>
591825ec
 + `clade_name` parameter added in `collapse` (2018-05-28, Mon)
   - <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/0H1PCJPlI1Q/DeZf9EVhBQAJ>
9f5ec41a
 + bug fixed of `gheatmap` for rowname subsetting is partial match in R
e4f92cb5
   (2018-05-23, Wed)
   - <https://github.com/GuangchuangYu/ggtree/issues/182>
 + compatible with ggplot2 2.2.1.9000 for `geom_text2(parse="emoji")`
e183e7d1
 + typo on vignettes (2018-05-08, Tue)
   - <https://github.com/GuangchuangYu/ggtree/pull/178>, thanks [@abichat](https://github.com/abichat)
50b227f1
 + compatible with ggplot2 2.2.1.9000 (2018-05-02, Wed)
   - incorporate newly introduce parameter `linejoin` and `arrow.fill` in `geom_segment`
 
 # ggtree 1.12.0
 
 + Bioconductor 3.7 release (2018-05-01, Tue)
 
8407d2ab
 # ggtree 1.11.6
cf8b3bfe
 
0b803ba8
 + reexport `treeio::read.iqtree` & `treeio::read.astral`(2018-04-17, Tue)
8407d2ab
 + now geom_treescale will plot the text that can **always** be separated from
   the bar (2018-03-07, Wed)
 + optimize daylight layout
     - <https://github.com/GuangchuangYu/ggtree/pull/165>
     - <https://github.com/GuangchuangYu/ggtree/pull/169>
40a372c1
 + geom_tiplab2 works with mapping = aes(subset) defined by users  (2018-02-24, Sta)
     - <https://groups.google.com/d/msgid/bioc-ggtree/72e18c5b-0ce5-4c25-80fa-3e2dabda8f72%40googlegroups.com>
d7cfc5a4
 + fixed overlapping branch after `flip`
     - <https://github.com/GuangchuangYu/ggtree/issues/167>
 
 # ggtree 1.11.5
 
a67ffa28
 + support passing `aes(subset)` in geom_tippoint (2018-01-30, Tue)
897c2ec4
 + support passing `aes(subset)` in geom_nodepoint (2018-01-26, Fri)
cf8b3bfe
 + fine tune y position after flip; flip compatible with collapse
     - <https://groups.google.com/d/msgid/bioc-ggtree/1d06342c-9645-4f71-9e66-7d7a7099bf0b%40googlegroups.com?utm_medium=email&utm_source=footer>
 
b681f0b4
 # ggtree 1.11.4
 
0266c285
 + re-implement collapse as collapse.ggtree method by importing dplyr::collapse
   generic to prevent function name collision (2018-01-03, Wed)
149acb32
 + update treeVisualization vignette, with more layout examples added (2017-12-22, Fri)
b681f0b4
 + update vignette (2017-12-21, Thu)
     - remove ggtreeUtilities.Rmd
     - merge treeAnnotation and advanceTreeAnnotation
149acb32