Changes in version 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. Changes in version 2.1.5 - bug fixed of calculating inset width and height - https://github.com/YuLab-SMU/ggtree/issues/289 Changes in version 2.1.4 - import aplot::xrange Changes in version 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 Changes in version 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 Changes in version 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 Changes in version 2.0.0 - Bioconductor 3.10 release (2019-10-30, Wed) Changes in version 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 Changes in version 1.99.0 - prepare for ggtree v=2.0.0 Changes in version 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 Changes in version 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) Changes in version 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 Changes in version 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) Changes in version 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) Changes in version 1.16.0 - Bioconductor 3.9 release Changes in version 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. Changes in version 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) Changes in version 1.15.4 - reimplement MRCA as a method inherited from tidytree (2019-01-10, Thu) - mv vignettes to treedata-book Changes in version 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 Changes in version 1.15.2 - compatible with tibble v=2.0.0 (2018-11-29, Thu) Changes in version 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 Changes in version 1.14.0 - Bioconductor 3.8 release Changes in version 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 Changes in version 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 Changes in version 1.13.3 - update viewClade according to the change of ggplot2 (2018-08-07, Tue) - https://github.com/GuangchuangYu/ggtree/issues/188 Changes in version 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 Changes in version 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 - compatible with ggplot2 2.2.1.9000 (2018-05-02, Wed) - incorporate newly introduce parameter linejoin and arrow.fill in geom_segment Changes in version 1.12.0 - Bioconductor 3.7 release (2018-05-01, Tue) Changes in version 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 Changes in version 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 Changes in version 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