# 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) # 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