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 treephylo
or treedata
objectyulab.utils::bib_ggtree()
for citation info (2024-07-27, Sat)yulab.utils::yulab_msg()
for startup message (2024-07-26, Fri)%<+%
operator to 'ggfun' (2024-05-28, Tue)geom_range()
(2024-04-07, Sun, #611)rect_to_poly()
from ggplot2 to make it compatible with ggplot2 3.5.0 (2024-02-13, Tue)rlang::check_installed()
to check whether the suggested pkg is installed (2023-08-11, Fri, #580)linewidth
parameter (synonyms for size
) in ggtree()
(2023-07-15, Sat, #574)branch.length = "none"
to plot 'hclust' object (2023-07-15, Sat, #574)ggtree()
supports 'dendro' object (ggdendro::dendro_data()
output) (2023-03-02, Thu)theme_dendrogram()
to use ggfun::theme_noxaxis()
(2022-11-21, Mon)cli::cli_alert_warning()
instead of warning_wrap
(2022-11-10, Thu)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)scale_color_subtree()
to the 'ggtreeDendro' package (2022-09-23, Fri)fortify
method for pvclust
object (2022-08-15, Mon)scale_color_subtree()
now supports passing a numeric value and internally it will call cutree(tree, k)
(2022-08-11, Thu)geom_tiplab
to better compatible with dendrogram layout (2022-06-23, Thu, #508)as.phylo.hclust2
to correct edge length as displayed in stats:::plot.hclust
(2022-06-21, Tue)branch.length = 'none'
(2022-04-29, Fri, #497)layout = 'radial'
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)identify()
method to 'ggfun' (2022-04-01, Fri)identify.gg()
to support 'ggplot' object and +xlim()
scale_color_subtree
and scale_colour_subtree
to color subtree via taxa group information (e.g., cutree, or kmeans) (2021-12-01, Wed)na.value = 'white'
in msaplot()
(2021-10-29, Fri)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)hclust
may generate negative tree heights) (2021-09-29, Wed; @xiangpin, #441, #445)ggdensitree
with align.tips=TRUE
sets max x to 0 (2021-09-26, Sun; @brj1, #437, #439)gheatmap
(2021-09-15, Wed, @matt-sd-watson, #434)nudge_x
parameter in geom_segment2
(2021-09-03, Fri; @xiangpin, #433)align
parameter in geom_hilight
(2021-08-30, Mon; @xiangpin, #431)data
parameter in geom_facet
now accepts function as input (2021-08-22, Sun; @xiangpin, #430)ggfun
and yulab.utils
(2021-08-20, Fri)options(layout.radial.linetype)
to set linetype of radial layout (either 'strainght' or 'curved') (2021-08-13, Fri; @xiangpin, #427)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 datageom_tiplab
supports fontface aesthetic (2021-07-06, Tue; @xiangpin)branch.y
and branch.x
geom_range
supports aes mapping (2021-06-04, Fri)geom_range
(2021-06-01, Tue)geom_nodelab
has a node="internal"
parameter. (2021-05-31, Mon)node = "external"
, it equivalent to `geom_tiplabnode = "all"
, it equivalent to list(geom_tiplab(), geom_nodelab())
geom_cladelab
(2021-05-10, Mon)extendto
argument for geom_hilight
now compatible with 'inward_circular' and 'dendrogram' layouts (2021-02-25, Thu)geom_rootpoint
(2021-01-08, Fri)label
and offset.label
introduced in geom_treescale
layer (2020-12-23, Wed)geom_rootedge
supports reversed x (2020-12-17, Thu)geom_nodelab()
now supports circular layout (2020-11-26, Thu)label_pad()
function to add padding characters to taxa labels (2020-10-09, Fri)family
parameter to geom_tiplab()
roundrect
and ellipse
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)td_unnest()
which return a function to flatten ggtree plot data (2020-09-14, Mon)geom_hilight
to support geom_hilight(data = mydata, node = selected_node)
(2020-09-03, Thu)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)geom_rootedge
and geom_point2
geom_hilight
to support geom_hilight(data = tbl_tree, node = selected_node)
. (2020-09-03, Thu)zoomClade
and geom_zoom_clade
to zoom in selected clade (2020-08-04, Tue)ggforce::facet_zoom
facet_labeller
according to the change of ggplot2
(2020-07-28, Tue)set_hilight_legend
as now geom_hilight
supports aesthetic mapping and can generate legend automotically 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)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)geom_hilight
to support aesthetic mapping (2020-07-22, Wed)geom_taxalink
to support aesthetic mapping (2020-07-20, Mon)layout_inward_circular
for layout_circular() + scale_x_reverse()
(2020-07-16, Thu)geom_taxalink
to support circular layout tree (2020-07-13, Mon).fortify
method for pvclust
object (2020-06-21, Mon)geom_hilight
and more detail messages of
warnings for extendto
. (2020-06-16, Tue)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)getYcoord_scale_category
(2020-05-13, Wed)geom_tiplab()
works with unrooted layouts (ape
, equal_angle
and daylight
) (2020-04-23, Thu)layoutEqualAngle
(2020-04-09, Thu)layoutEqualAngle
. aplot::xrange
xlim2
and ylim2
to aplot package (2020-03-30, Mon)mutate_
as it was deprecated in dplyr (2020-03-25, Wed)expand_scale
was deprecated in ggplot2 v=3.3.0, import expansion
instead (2020-03-12, Thu)ggplot(tree) + geom_tiplab()
(2020-01-26, Sun)coord_fixed
by default (2020-01-25, Sat)layout = "ape"
, use ape unrooted layout geom_highlight
as an alias of geom_hilight
(2020-01-08, Wed)clip="off"
for all layouts (2019-12-06, Fri)fontface
if geom
is image
or phylopic
in geom_tiplab
and geom_nodelab
(2019-11-29, Fri)guide_legend
, scale_colour_manual
, scale_color_manual
, scale_fill_manual
and margin
from ggplot2
offspring
method for ggtree
object (2019-11-21, Thu)revts
to work with collapse
(2019-11-18, Mon)xlim2
and ylim2
to support discrete scale.xlim2
and ylim2
to uniformize axis limits of ggplot objects (2019-10-31, Thu)fontface
warning message when align=TRUE
in geom_tiplab
(2019-10-30, Wed)geom_hilight
for tree$edge.length = NULL
(2019-10-16, Wed)fortify
method for igraph (only work with tree graph) (2019-09-28, Sat)ggdensitree
(2019-09-11, Wed)fortify
methods for hierarchical clustering objects, including agnes
, diana
and twins
(2019-08-30, Fri) geom_hilight
supports unrooted
and daylight
layouts (2019-08-28, Wed)geom_hilight_encircle
geom_motif
according to the change of gggenes
and allow labeling genes (2019-08-27, Tue)geom_strip
with more robust support of labelling strip, either input taxa using name or id.phylog
defined in ade4 package (2019-08-14, Wed)geom_cladelabel
supports unrooted
and daylight
layouts (2019-08-14, Wed)geom_cladelabel2
nodelab
method for ggtree to convert node number to label (2019-08-09, Fir)nodeid
as S3 generic in tidytree
v=0.2.6 nodeid
function for tree object to treeiogzoom
functionrootnode
parameter in geom_tree
with default = TRUE and behave as previous version (2019-08-08, Thu)rootnode = FALSE
, there will be no line segment of root to itself.gheatmap
to support collapsed node (2019-08-06, Tue)hclust
and dendrogram
(2019-07-31, Wed)layout_circular
, layout_fan
and layout_rectangular
layout_dendrogram
and theme_dendrogram
scale_x_range
for adding second x-axis for geom_range
(2019-07-23, Tue)branch.length
parameter to center
for geom_range
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)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)root.position
parameter for fortify
and ggtree
(2019-05-27, Mon)geom_facet
, a geom layer version of facet_plot
(2019-05-23, Thu)scale_x_ggtree
, now we can use gheatmap() + scale_x_ggtree()
(2019-05-22, Wed)xlim_expand
to work with ggplot2
(2019-05-20, Tue)legend_title
variable in gheatmap
(2019-05-16, Thu)geom_range
(2019-04-27, Sat)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)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)ggplotify::as.ggplot(grid_object)
, so it is not the original ggtree
object.theme_tree2
(2019-01-14, Mon)rescale_tree
to treeio
(2019-01-11, Fri)MRCA
as a method inherited from tidytree
(2019-01-10, Thu)reroot
method to treeio
package and rename to root
(2018-12-28, Fri)branch.length="none"
in unrooted layouts (2018-12-26, Wed)tibble
v=2.0.0 (2018-11-29, Thu)revts
also reverse the branch
column (2018-11-11, Sun)msaplot
. (2018-11-07, Wed)scale_y_continuous(expand = c(0, 0))
for gheatmap
when colnames = FALSE
(2018-10-17, Wed)geom_rootedge
(2018-09-13, Thu)facet_labeller
to label panels of facet_plot
output (2018-09-10, Mon)viewClade
according to the change of ggplot2
(2018-08-07, Tue)viewClade
(2018-07-21, Sat)facet_plot
by adding description and example (2018-07-19, Thu)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)ggplot2::fortify
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)clade_name
parameter added in collapse
(2018-05-28, Mon)gheatmap
for rowname subsetting is partial match in R
(2018-05-23, Wed)geom_text2(parse="emoji")
linejoin
and arrow.fill
in geom_segment
treeio::read.iqtree
& treeio::read.astral
(2018-04-17, Tue)flip
aes(subset)
in geom_tippoint (2018-01-30, Tue)aes(subset)
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