# ggtree 2.5.1

 + update man file of `geom_rootpoint` (2021-01-08, Fri)

 + `label` and `offset.label` introduced in `geom_treescale` layer (2020-12-23, Wed)
   - <https://github.com/YuLab-SMU/ggtree/pull/360>
 + `geom_rootedge` supports reversed x (2020-12-17, Thu)
   - <https://github.com/YuLab-SMU/ggtree/pull/358>

 + `geom_nodelab()` now supports circular layout (2020-11-26, Thu)
   - <https://github.com/YuLab-SMU/ggtree/issues/352>
   - <https://github.com/YuLab-SMU/ggtree/pull/353>

 + branch size can be grandualy changed (2020-10-29, Thu)
   - <https://github.com/YuLab-SMU/ggtree/pull/349>

 # ggtree 2.4.0
 
 + Bioconductor 3.12 release (2020-10-28, Wed)
 

 # ggtree 2.3.7

 
 + add `label_pad()` function to add padding characters to taxa labels (2020-10-09, Fri)
   - <https://groups.google.com/g/bioc-ggtree/c/INJ0Nfkq3b0/m/lXefnfV5AQAJ>
 + add `family` parameter to `geom_tiplab()` 
 

 # ggtree 2.3.6

 + new layouts, `roundrect` and `ellipse`
   - <https://github.com/YuLab-SMU/ggtree/pull/344>
   - <https://github.com/YuLab-SMU/ggtree/pull/346>

 + `fortify()` method for `treedataList` object (2020-09-20, Sun)

 + `vexpand()` and `ggexpand()` to expand plot limit by ratio of plot range (2020-09-18, Fri) 
 + `geom_cladelab()`, an updated version of `geom_cladelabel` that supports aes mapping (2020-09-17, Thu)

   - <https://github.com/YuLab-SMU/ggtree/pull/342>
 

 # ggtree 2.3.5

 + `td_unnest()` which return a function to flatten ggtree plot data (2020-09-14, Mon)
   - <https://yulab-smu.top/treedata-book/chapter12.html#td_unnest>

 + update `geom_hilight` to support `geom_hilight(data = mydata, node = selected_node)` (2020-09-03, Thu)

 + Defunct `geom_nodelab2()` (2020-09-02, Wed)
 + `geom_tiplab()` and `geom_nodelab()` support `geom = "shadowtext"` 

 + `td_filter()` which return a function to subset ggtree plot data in geom layers (2020-08-29, Sat)
   - <https://yulab-smu.top/treedata-book/chapter12.html#td_filter>

 + update man files of `geom_rootedge` and `geom_point2`

 + update `geom_hilight` to support `geom_hilight(data = tbl_tree, node = selected_node)`. (2020-09-03, Thu)

 # ggtree 2.3.4

 + `zoomClade` and `geom_zoom_clade` to zoom in selected clade (2020-08-04, Tue)
   - these two functions are wrapper function of `ggforce::facet_zoom`

 + update `facet_labeller` according to the change of `ggplot2` (2020-07-28, Tue)
 + defunct `set_hilight_legend` as now `geom_hilight` supports aesthetic mapping and can generate legend automotically 

 + remove `annotation_image`, `phylopic` and `subview` as they were defunct for quite a long time. Users should refer to the `ggimage` package if they want to annotate tree with image or subplots.
 + `as_ylab` parameter added in `geom_tiplab()`, which supports displaying tip labels as y-axis label and only works for rectangular and dendrogram layouts 

 + `hexpand` to expand x limits by ratio of x range and supports both direction (1 for rhs and -1 for lhs) (2020-07-27, Mon)
 

 # ggtree 2.3.3

 + add `type` parameter in `geom_hilight`, default is `auto`, optional `rect` 
   to `rectangular` layer, `encircle` to `encircle` layer and comment original 
   `geom_hilight`, and support `subset` in aesthetic. (2020-07-23, Thu)

 + update `geom_hilight` to support aesthetic mapping (2020-07-22, Wed)

 + update `geom_taxalink` to support aesthetic mapping (2020-07-20, Mon)

 + `layout_inward_circular` for `layout_circular() + scale_x_reverse()` (2020-07-16, Thu)
 

 # ggtree 2.3.2
 
 + update `geom_taxalink` to support circular layout tree (2020-07-13, Mon).
 

 # ggtree 2.3.1

 + `fortify` method for `pvclust` object (2020-06-21, Mon)

 + add dot parameters for color or size of `geom_hilight` and more detail messages of
   warnings for `extendto`. (2020-06-16, Tue)

 + modified the angle of clade labels. Added horizontal parameter to control
   whether set clade labels to horizontal. When the parameter was set to `FALSE`, 
   it will be useful for the layouts in `coord_polar`, such as `circular`, `fan`,

   `radial`. To better view the clade labels, their angles has been adjusted. (2020-06-15, Mon)

 + bug fixed in `getYcoord_scale_category` (2020-05-13, Wed)
 
 # ggtree 2.2.0
 
 + Bioconductor 3.11 release
 

 # ggtree 2.1.6

 + Now `geom_tiplab()` works with unrooted layouts (`ape`, `equal_angle` and `daylight`) (2020-04-23, Thu)
   - <https://github.com/YuLab-SMU/ggtree/issues/292>

 + bug fixed of `layoutEqualAngle` (2020-04-09, Thu)
   - in tibble v=3.0.0, df$x = NA will store df$x as lgl variable and assign numeric value to df$x will throw error. Now change to df$x = 0 in `layoutEqualAngle`. 

 
 # ggtree 2.1.5
 
 + bug fixed of calculating inset width and height

   - <https://github.com/YuLab-SMU/ggtree/issues/289>

 # ggtree 2.1.4
 
 + import `aplot::xrange` 
 

 # ggtree 2.1.3
 

 + move `xlim2` and `ylim2` to aplot package (2020-03-30, Mon)
   - <https://cran.r-project.org/package=aplot>

 + remove `mutate_` as it was deprecated in dplyr (2020-03-25, Wed)

 + fixed mutate bug caused by new version of dplyr and tidytree in daylight layout (2020-03-16, Mon)
   - <https://github.com/YuLab-SMU/ggtree/issues/282>

 # ggtree 2.1.2
 

 + `expand_scale` was deprecated in ggplot2 v=3.3.0, import `expansion` instead (2020-03-12, Thu)

 + bug fixed of determined layout for `ggplot(tree) + geom_tiplab()` (2020-01-26, Sun)
   - <https://github.com/YuLab-SMU/ggtree/issues/272>
 + set unrooted layout to use `coord_fixed` by default (2020-01-25, Sat)
 + if `layout = "ape"`, use ape unrooted layout 

   - <https://github.com/YuLab-SMU/ggtree/pull/273>

 # ggtree 2.1.1
 

 + export `geom_highlight` as an alias of `geom_hilight` (2020-01-08, Wed)

 + set `clip="off"` for all layouts (2019-12-06, Fri)

 + not passing `fontface` if `geom` is `image` or `phylopic` in `geom_tiplab` and `geom_nodelab` (2019-11-29, Fri)
 + import and re-export `guide_legend`, `scale_colour_manual`, `scale_color_manual`, `scale_fill_manual` and `margin` from `ggplot2`

 + `offspring` method for `ggtree` object (2019-11-21, Thu)

 + fixed `revts` to work with `collapse` (2019-11-18, Mon)

 + convert roxygen documents using markdown (2019-11-01, Fri)

 + extend `xlim2` and `ylim2` to support discrete scale.

 + `xlim2` and `ylim2` to uniformize axis limits of ggplot objects (2019-10-31, Thu)

   - <https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plot>

   - <https://yulab-smu.github.io/treedata-book/docs/chapter10.html#axis_align>

 + 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)
 

 # ggtree 1.99.1
 

 + 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>

 + `fortify` method for igraph (only work with tree graph) (2019-09-28, Sat)

 + `ggdensitree` (2019-09-11, Wed)
   - <https://github.com/YuLab-SMU/ggtree/pull/253>

   - <https://github.com/YuLab-SMU/ggtree/pull/255> 
   - <https://yulab-smu.github.io/treedata-book/chapter4.html#visualize-a-list-of-trees>
 

 # ggtree 1.99.0
 
 + prepare for ggtree v=2.0.0
 

 # ggtree 1.17.5
 

 + `fortify` methods for hierarchical clustering objects, including `agnes`, `diana` and `twins` (2019-08-30, Fri) 

 + now `geom_hilight` supports `unrooted` and `daylight` layouts (2019-08-28, Wed)

   - by calling `geom_hilight_encircle`

 + 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>

 + re-implement `geom_strip` with more robust support of labelling strip, either input taxa using name or id.

 + support `phylog` defined in ade4 package (2019-08-14, Wed)

   - <https://yulab-smu.github.io/treedata-book/chapter9.html#phylog>

 # ggtree 1.17.4
 

 + now `geom_cladelabel` supports `unrooted` and `daylight` layouts (2019-08-14, Wed)
   - by integrating `geom_cladelabel2`

 + 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

 + defunct `gzoom` function
 + introduce `rootnode` parameter in `geom_tree` with default = TRUE and behave as previous version (2019-08-08, Thu)

   - the invisible root to itself line segment have advantage for the number of line segments is consistent with the number of nodes. 

   - if `rootnode = FALSE`, there will be no line segment of root to itself.

 + extend `gheatmap` to support collapsed node (2019-08-06, Tue)
   - <https://github.com/GuangchuangYu/ggtree/pull/243>

 + support `hclust` and `dendrogram` (2019-07-31, Wed)
 

 # ggtree 1.17.3
 

 + 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>

 + `scale_x_range` for adding second x-axis for `geom_range` (2019-07-23, Tue)
 + change `branch.length` parameter to `center` for `geom_range`
 

 # ggtree 1.17.2
 

 + extend `expand` according to the change of `collapse` (2019-07-11, Thu)
 + `mode` parameter in `collapse`

 + `geom_tiplab` now works with 'circular' and 'fan' layouts (2019-07-05, Fri)

 + `geom_inset` for adding subplots to specific nodes (see also the `inset` function introduced in v=1.3.8)

 # ggtree 1.17.1
 

 + `facet_data` to extract data used in `facet_plot` or `geom_facet` (2019-07-02, Tue)

 + `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>

 + `root.position` parameter for `fortify` and `ggtree` (2019-05-27, Mon)

 + `geom_facet`, a geom layer version of `facet_plot` (2019-05-23, Thu)

 + update `scale_x_ggtree`, now we can use `gheatmap() + scale_x_ggtree()` (2019-05-22, Wed)

 + extend `xlim_expand` to work with `ggplot2` (2019-05-20, Tue)
   - <https://yulab-smu.github.io/treedata-book/chapter9.html#xlim_expand>

 + add `legend_title` variable in `gheatmap` (2019-05-16, Thu)
 
 # ggtree 1.16.0
 
 + Bioconductor 3.9 release
 

 # ggtree 1.15.6
 

 + compatible with range is NULL in `geom_range` (2019-04-27, Sat)
   - <https://groups.google.com/d/msg/bioc-ggtree/yNzjtioVVGU/MCh3MPl_CwAJ>

 + 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)

 + remove `get.offspring.df` and `get.offspring.tip` and instead use `tidytree::offspring` (2019-01-28, Mon)

 + `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.
 

 # ggtree 1.15.5
 

 + bug fixed of `theme_tree2` (2019-01-14, Mon)
   - <https://github.com/GuangchuangYu/ggtree/issues/218>  

 + mv `rescale_tree` to `treeio` (2019-01-11, Fri)
 

 # 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/) 
 

 # ggtree 1.15.3
 

 + move `reroot` method to `treeio` package and rename to `root` (2018-12-28, Fri)

 + bug fixed for setting `branch.length="none"` in unrooted layouts (2018-12-26, Wed)
   - bug introduced in <https://github.com/GuangchuangYu/ggtree/pull/201>
 

 # ggtree 1.15.2
 
 + compatible with `tibble` v=2.0.0 (2018-11-29, Thu)
 

 # ggtree 1.15.1
 

 + 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>

 + 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
 

 # ggtree 1.13.6
 

 + set `scale_y_continuous(expand = c(0, 0))` for `gheatmap` when `colnames = FALSE` (2018-10-17, Wed)
   - <https://github.com/GuangchuangYu/ggtree/issues/204>

 + made data usable with treedata in 'equal_angle' and 'daylight' layouts (2018-10-11, Thu)
   - <https://github.com/GuangchuangYu/ggtree/pull/201>
   

 # ggtree 1.13.5

 + enable additional parameters passed to `geom_rootedge` (2018-09-13, Thu)
   - <https://github.com/GuangchuangYu/ggtree/issues/195>

 + `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>
   

 # ggtree 1.13.3
 
 + update `viewClade` according to the change of `ggplot2` (2018-08-07, Tue)
   - <https://github.com/GuangchuangYu/ggtree/issues/188>
   

 # ggtree 1.13.2

 + xmax_adjust  in `viewClade` (2018-07-21, Sat)
   - <https://github.com/GuangchuangYu/ggtree/issues/187>

 + update rd of `facet_plot` by adding description and example (2018-07-19, Thu)

 + order by y in `facet_plot` (2018-07-09, Mon)

 + `extend` parameter in `geom_cladelabel` and `geom_strip` supports specifying
   extension of both sides (2018-07-06, Fri)

 + `geom_nodelab2` for circular layout (2018-07-03, Tue)
   - <https://groups.google.com/d/msgid/bioc-ggtree/cbe5e1e3-99c4-481d-8523-d5b50cf0460b%40googlegroups.com>

 + re-export `ggplot2::fortify`
   - <https://groups.google.com/d/msgid/bioc-ggtree/bf7a9b3c-9a8f-4d8d-a782-1b467fba38bc%40googlegroups.com>
 

 # ggtree 1.13.1

 + `geom_nodepoint` & `geom_tippoint` now compatible with `ggplot2` v 2.2.1 &

   3.0.0 (2018-06-26, Tue)

 + `geom_rootedge` (2018-06-13, Wed)
   - <https://github.com/GuangchuangYu/ggtree/issues/183>

 + `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>

 + bug fixed of `gheatmap` for rowname subsetting is partial match in R

   (2018-05-23, Wed)
   - <https://github.com/GuangchuangYu/ggtree/issues/182>
 + compatible with ggplot2 2.2.1.9000 for `geom_text2(parse="emoji")`

 + typo on vignettes (2018-05-08, Tue)
   - <https://github.com/GuangchuangYu/ggtree/pull/178>, thanks [@abichat](https://github.com/abichat)

 + 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)
 

 # ggtree 1.11.6

 + reexport `treeio::read.iqtree` & `treeio::read.astral`(2018-04-17, Tue)

 + 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>

 + 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>

 + fixed overlapping branch after `flip`
     - <https://github.com/GuangchuangYu/ggtree/issues/167>
 
 # ggtree 1.11.5
 

 + support passing `aes(subset)` in geom_tippoint (2018-01-30, Tue)

 + support passing `aes(subset)` in geom_nodepoint (2018-01-26, Fri)

 + 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>
 

 # ggtree 1.11.4
 

 + re-implement collapse as collapse.ggtree method by importing dplyr::collapse
   generic to prevent function name collision (2018-01-03, Wed)

 + update treeVisualization vignette, with more layout examples added (2017-12-22, Fri)

 + update vignette (2017-12-21, Thu)
     - remove ggtreeUtilities.Rmd
     - merge treeAnnotation and advanceTreeAnnotation