NEWS.md

In GuangchuangYu/ggtree: an R package for visualization of tree and annotation data

ggtree 3.14.0

• Bioconductor RELEASE_3_20 (2024-10-30, Wed)

ggtree 3.13.2

• mv td_filter(), td_unnest() and td_mutate() to 'ggfun' package (2024-10-24, Thu)

ggtree 3.13.1

• layout argument can be a function to re-calculate the coord of nodes (2024-07-27, Sat, #622)
• layout.params = list(as.graph=TRUE) (by default) for converting the tree to a graph tree (igraph object), so that graph layout can be directly applied to visualize a tree
• otherwise, the function can assume the input tree as a phylo or treedata object
• use yulab.utils::yulab_msg() for startup message (2024-07-26, Fri)
• mv %<+% operator to 'ggfun' (2024-05-28, Tue)

ggtree 3.12.0

• Bioconductor RELEASE_3_19 (2024-05-14, Tue)

ggtree 3.11.2

• expose 'position' parameter for geom_range() (2024-04-07, Sun, #611)

ggtree 3.11.1

• copy rect_to_poly() from ggplot2 to make it compatible with ggplot2 3.5.0 (2024-02-13, Tue)

ggtree 3.10.0

• Bioconductor RELEASE_3_18 (2023-10-25, Wed)

ggtree 3.9.1

• use rlang::check_installed() to check whether the suggested pkg is installed (2023-08-11, Fri, #580)
• allows using linewidth parameter (synonyms for size) in ggtree() (2023-07-15, Sat, #574)
• bug fixed in setting branch.length = "none" to plot 'hclust' object (2023-07-15, Sat, #574)

ggtree 3.8.0

• Bioconductor RELEASE_3_17 (2023-05-03, Wed)

ggtree 3.7.2

• ggtree() supports 'dendro' object (ggdendro::dendro_data() output) (2023-03-02, Thu)
• update theme_dendrogram() to use ggfun::theme_noxaxis() (2022-11-21, Mon)
• using cli::cli_alert_warning() instead of warning_wrap (2022-11-10, Thu)

ggtree 3.7.1

• compatible with ggplot2 v=3.4.0 (2022-11-07, Mon)
• allows setting options(clade_align = TRUE) to align geom_hilight() layer and allows setting options(clade_width_extend = 0.35) to set the amount the width extension (in y-axis) of geom_hilight(). These two features is designed for ggtreeDendro::geom_rect_subtree() layer (2022-11-06, Sun)

ggtree 3.6.0

• Bioconductor RELEASE_3_16 (2022-11-02, Wed)

ggtree 3.5.3

• add new citation (the iMeta 2022 paper) (2022-09-26, Mon)
• move scale_color_subtree() to the 'ggtreeDendro' package (2022-09-23, Fri)
• update fortify method for pvclust object (2022-08-15, Mon)
• add citation of the tree data book (2022-08-13, Sat)

ggtree 3.5.2

• scale_color_subtree() now supports passing a numeric value and internally it will call cutree(tree, k) (2022-08-11, Thu)
• support 'linkage' class defined in the 'mdendro' package (2022-08-11, Thu)
• clone the plot environment before assigning layout (2022-07-19, Tue, #516)
• bug fixed in 'equal_angle' layout (2022-07-08, Fri, #514)
• optimize geom_tiplab to better compatible with dendrogram layout (2022-06-23, Thu, #508)

ggtree 3.5.1

• as.phylo.hclust2 to correct edge length as displayed in stats:::plot.hclust (2022-06-21, Tue)
• add outline to nodepies (2022-06-20, Mon, #506)
• new 'slanted' layout for branch.length = 'none' (2022-04-29, Fri, #497)
  • only works for Cartesian coordination, that means it will not work for layout = 'radial'

ggtree 3.4.0

• Bioconductor 3.15 release (2022-04-28, Thu)

ggtree 3.3.3

• geom_striplab() that supports aes() mapping (2022-04-22, Fri, #493)
• to.bottom parameter introduced in geom_hilight() to allow the highlight layer was added into the lowest layer stack (2022-04-22, Fri, #492)

ggtree 3.3.2

• mv identify() method to 'ggfun' (2022-04-01, Fri)
• update identify.gg() to support 'ggplot' object and +xlim()
• update man files (2022-03-23, Wed, #489)

ggtree 3.3.1

• use graph layouts to visualize tree (2021-12-10, Fri, #460, #461)
• igraph layout
• graphlayouts: https://cran.r-project.org/web/packages/graphlayouts/index.html
• scale_color_subtree and scale_colour_subtree to color subtree via taxa group information (e.g., cutree, or kmeans) (2021-12-01, Wed)
• set na.value = 'white' in msaplot() (2021-10-29, Fri)

ggtree 3.2.0

• Bioconductor 3.14 release

ggtree 3.1.6

• geom_cladelab now supports extend parameter as in geom_cladelabel (2021-10-14, Thu, @xiangpin, #446)
• geom_hilight supports fill linear gradient colour and round rect background (2021-10-11, Mon; @xiangpin, #449, #444)
• work with negative edge lengths (hclust may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441, #445)

ggtree 3.1.5

• ggdensitree with align.tips=TRUE sets max x to 0 (2021-09-26, Sun; @brj1, #437, #439)
• custom column headers for gheatmap (2021-09-15, Wed, @matt-sd-watson, #434)
• bug fixed of nudge_x parameter in geom_segment2 (2021-09-03, Fri; @xiangpin, #433)

ggtree 3.1.4

• introduce align parameter in geom_hilight (2021-08-30, Mon; @xiangpin, #431)
• the data parameter in geom_facet now accepts function as input (2021-08-22, Sun; @xiangpin, #430)
• import ggfun and yulab.utils (2021-08-20, Fri)
• allow using options(layout.radial.linetype) to set linetype of radial layout (either 'strainght' or 'curved') (2021-08-13, Fri; @xiangpin, #427)

ggtree 3.1.3

• data argument in geom_tiplab and position argument in geom_tree (2021-08-10, Tue; #426, @xiangpin)
• geom_hilight and geom_cladelab supports function as input data (2021-07-28, Wed; #421, @xiangpin)
• td_mutate for mutating tree data
• geom_tiplab supports fontface aesthetic (2021-07-06, Tue; @xiangpin)

ggtree 3.1.2

• calculate branch mid point for unrooted layout tree (2021-06-11, Fri)
• branch.y and branch.x
• geom_range supports aes mapping (2021-06-04, Fri)

ggtree 3.1.1

• bug fixed in geom_range (2021-06-01, Tue)
• https://github.com/YuLab-SMU/ggtree/pull/410
• now geom_nodelab has a node="internal" parameter. (2021-05-31, Mon)
• if node = "external", it equivalent to `geom_tiplab
• if node = "all", it equivalent to list(geom_tiplab(), geom_nodelab())

ggtree 3.0.0

• Bioconductor 3.13 relese

ggtree 2.5.3

• optimize text angle in geom_cladelab (2021-05-10, Mon)
• https://github.com/YuLab-SMU/ggtree/pull/396

ggtree 2.5.2

• extend 'continuous' parameter to support 4 possible values, i.e., 'none' to disable continuous transition, 'color' (or 'colour') to enable continuous color transition, 'size' to enable continuous size (branch thickness) transition and 'all' to enable continuous color and size transition (2021-04-07, Wed)
• https://github.com/YuLab-SMU/ggtree/pull/385
• https://github.com/YuLab-SMU/ggtree/pull/387
• extendto argument for geom_hilight now compatible with 'inward_circular' and 'dendrogram' layouts (2021-02-25, Thu)
• https://github.com/YuLab-SMU/ggtree/pull/379

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

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
• 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

GuangchuangYu/ggtree documentation built on Oct. 31, 2024, 10:10 a.m.