ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Version 1.8.1

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.

Browse man pages Browse package API and functions Browse package files

AuthorGuangchuang Yu [aut, cre, cph], Tommy Tsan-Yuk Lam [aut, ths], Justin Silverman [ctb]
Bioconductor views Alignment Annotation Clustering DataImport MultipleSequenceAlignment ReproducibleResearch Software Visualization
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version1.8.1
URL https://guangchuangyu.github.io/ggtree
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ggtree")

Man pages

add_colorbar: add_colorbar
add-TREEDATA: %<+%
add_TREEINFO: %+>%
annotation_image: annotation_image
apeBoot: apeBoot
applyLayoutDaylight: applyLayoutDaylight
as.binary: as.binary
as.data.frame.phylo: as.data.frame
as.polytomy: as.polytomy
collapse: collapse
Date2decimal: Date2decimal
decimal2Date: decimal2Date
dotFun: .
download.phylopic: download.phylopic
expand: expand
facet_plot: facet_plot
flip: flip
fortify: fortify
geom_aline: geom_aline
geom_balance: geom_balance
geom_cladelabel: geom_cladelabel
geom_hilight: geom_hilight
geom_label2: geom_label2
geom_nodepoint: geom_nodepoint
geom_point2: geom_point2
geom_range: geom_range
geom_rootpoint: geom_rootpoint
geom_segment2: geom_segment2
geom_strip: geom_strip
geom_taxalink: geom_taxalink
geom_text2: geom_text2
geom_tiplab: geom_tiplab
geom_tiplab2: geom_tiplab2
geom_tippoint: geom_tippoint
geom_tree: geom_tree
geom_tree2: geom_tree2
geom_treescale: geom_treescale
get_balance_position: get_balance_position
getChild.df: getChild.df
get_clade_position: get_clade_position
get_heatmap_column_position: get_heatmap_column_position
getNodeAngle.df: getNodeAngle.df
getNodesBreadthFirst.df: getNodesBreadthFirst.df
get.offspring.tip: get.offspring.tip
getParent.df: getParent.df
get.path: get.path
get.phylopic: get.phylopic
getSubtree: getSubtree
GetSubtree.df: GetSubtree.df
GetSubtreeUnrooted: GetSubtreeUnrooted
getSubtreeUnrooted.df: GetSubtreeUnrooted
get_taxa_name: get_taxa_name
getTreeArcAngles: getTreeArcAngles
ggtree: visualizing phylogenetic tree and heterogenous associated...
ggtree-ggproto: StatBalance
gheatmap: gheatmap
groupClade-methods: groupClade method
groupOTU-methods: groupOTU method
gzoom-methods: gzoom method
gzoom.phylo: gzoom
identify: identify
inset: inset
layoutDaylight: Equal daylight layout method for unrooted trees.
layoutEqualAngle: layoutEqualAngle
MRCA: MRCA
msaplot: msaplot
multiplot: multiplot
NJ: NJ
nodebar: nodebar
nodeid: nodeid
nodepie: nodepie
open_tree: open_tree
phylopic: phylopic
pipe: pipe
print.beastList: print
reroot-methods: reroot method
rescale_tree: rescale_tree
revts: revts
rm.singleton.newick: rm.singleton.newick
rotate: rotate
rotate_tree: rotate_tree
rotateTreePoints.df: rotateTreePoints.data.fram
scaleClade: scaleClade
scale_color-methods: scale_color method
scale_x_ggtree: scale_x_ggtree
stat_balance: stat_balance
stat_hilight: stat_hilight
subview: subview
theme_inset: theme_inset
theme_transparent: theme_transparent
theme_tree: theme_tree
theme_tree2: theme_tree2
update-TREE: %<%
viewClade: viewClade
xlim_expand: xlim_expand
xlim_tree: xlim_tree

Functions

. Man page
Date2decimal Man page Source code
GetSubtree.df Man page Source code
GetSubtreeUnrooted Man page Source code
MRCA Man page Source code
NJ Man page Source code
StatBalance Man page
StatHilight Man page
\%+>\% Man page
\%<+\% Man page
\%<\% Man page
\%>\% Man page
add_angle_slanted Source code
add_colorbar Man page Source code
add_panel Source code
annotation_image Man page Source code
apeBoot Man page Source code
applyLayoutDaylight Man page Source code
as.binary Man page Source code
as.binary.phylo Man page Source code
as.data.frame.phylo Man page Source code
as.data.frame.phylo_ Source code
as.data.frame.treedata Source code
as.data.frame_ Source code
as.polytomy Man page Source code
assign_child_status Source code
assign_parent_status Source code
calculate_angle Source code
calculate_branch_mid Source code
collapse Man page Source code
color_scale Source code
coplot Source code
decimal2Date Man page Source code
download.phylopic Man page Source code
download.phylopic_internal Source code
expand Man page Source code
extract.treeinfo.jplace Source code
facet_plot Man page Source code
flip Man page Source code
fortify.beast Source code
fortify.codeml Source code
fortify.codeml_mlc Source code
fortify.codeml_mlc_ Source code
fortify.jplace Source code
fortify.multiPhylo Source code
fortify.obkData Source code
fortify.paml_rst Source code
fortify.phylip Source code
fortify.phylo Man page Source code
fortify.phylo4 Source code
fortify.phylo4d Source code
fortify.phyloseq Source code
fortify.r8s Source code
fortify.treedata Source code
geom_aline Man page Source code
geom_balance Man page Source code
geom_cladelabel Man page Source code
geom_hilight Man page Source code
geom_label2 Man page Source code
geom_nodepoint Man page Source code
geom_point2 Man page Source code
geom_range Man page Source code
geom_rootpoint Man page Source code
geom_segment2 Man page Source code
geom_strip Man page Source code
geom_taxalink Man page Source code
geom_text2 Man page Source code
geom_tiplab Man page Source code
geom_tiplab2 Man page Source code
geom_tippoint Man page Source code
geom_tipsegment Source code
geom_tree Man page Source code
geom_tree2 Man page Source code
geom_treescale Man page Source code
get.ancestor.df Source code
get.offspring.df Source code
get.offspring.tip Man page Source code
get.path Man page Source code
get.path_length Source code
get.phylopic Man page Source code
get.trunk Source code
getAR Source code
getAncestor Source code
getAncestor.df Source code
getChild Source code
getChild.df Man page Source code
getCols Source code
getIdx Source code
getIdx_internal Source code
getMRCA.df Source code
getMRCA.df_internal Source code
getNodeAngle.df Man page Source code
getNodeName Source code
getNodesBreadthFirst.df Man page Source code
getNodes_by_postorder Source code
getParent Source code
getParent.df Man page Source code
getRoot.df Source code
getSibling Source code
getSubtree Man page Source code
getSubtreeUnrooted.df Man page Source code
getTreeArcAngles Man page Source code
getXYcoord_slanted Source code
getXcoord Source code
getXcoord2 Source code
getXcoord_no_length Source code
getYcoord Source code
getYcoord_scale Source code
getYcoord_scale2 Source code
getYcoord_scale_category Source code
getYcoord_scale_numeric Source code
get_balance_position Man page Source code
get_balance_position_ Source code
get_clade_position Man page Source code
get_clade_position_ Source code
get_cladelabel_position Source code
get_cladelabel_position_ Source code
get_color_attribute Source code
get_heatmap_column_position Man page Source code
get_striplabel_position Source code
get_striplabel_position_ Source code
get_taxa_name Man page Source code
get_tipsegment_position Source code
get_tree_data Source code
get_tree_view Source code
get_treescale_position Source code
gfocus.df Source code
ggpie Source code
ggtree Man page Source code
ggtree-package Man page
gheatmap Man page Source code
groupClade Man page
groupClade,ggtree-method Man page
groupClade.df Source code
groupClade.ggtree Source code
groupOTU Man page
groupOTU,ggtree-method Man page
groupOTU.df Source code
groupOTU.ggtree Source code
gzoom Man page
gzoom,beast-method Man page
gzoom,codeml-method Man page
gzoom,ggtree-method Man page
gzoom,paml_rst-method Man page
gzoom,phylo-method Man page
gzoom,treedata-method Man page
gzoom.ggtree Source code
gzoom.phylo Man page Source code
identify.gg Man page Source code
inset Man page Source code
is.tree Source code
is.tree_attribute Source code
is.tree_attribute_ Source code
isRoot Source code
isTip Source code
isTip.df Source code
layout.unrooted Source code
layoutDaylight Man page Source code
layoutEqualAngle Man page Source code
layout_circular Source code
merge_phylo_anno.codeml_mlc Source code
merge_phylo_anno.paml_rst Source code
msaplot Man page Source code
multiplot Man page Source code
nodebar Man page Source code
nodeid Man page Source code
nodeid.gg Source code
nodeid.tree Source code
nodepie Man page Source code
onAttach Source code
open_tree Man page Source code
package-ggtree Man page
phylopic Man page Source code
plot_fantree Source code
plot_fantrees Source code
print.beastList Man page Source code
re_assign_ycoord_df Source code
reassign_y_from_node_to_root Source code
reroot Man page
reroot,beast-method Man page
reroot,phylo-method Man page
reroot_node_mapping Source code
rescale_tree Man page Source code
reverse.treeview Source code
reverse.treeview.data Source code
revts Man page Source code
rm.singleton.newick Man page Source code
rotate Man page Source code
rotateTreePoints.df Man page Source code
rotate_tree Man page Source code
roundDigit Source code
scaleClade Man page Source code
scaleX_by_time Source code
scaleX_by_time_from_mrsd Source code
scaleY Source code
scale_color Man page
scale_color,beast-method Man page
scale_color,paml_rst-method Man page
scale_color,phylo-method Man page
scale_color,treedata-method Man page
scale_color_ Source code
scale_x_ggtree Man page Source code
set_branch_length Source code
setup_tree_data Source code
stat_balance Man page Source code
stat_cladeBar Source code
stat_cladeText Source code
stat_hilight Man page Source code
stat_stripBar Source code
stat_stripText Source code
stat_tree Source code
stat_treeScaleLine Source code
stat_treeScaleText Source code
subview Man page Source code
supported_tree_object Source code
taxa2node Source code
theme_inset Man page Source code
theme_transparent Man page Source code
theme_tree Man page Source code
theme_tree2 Man page Source code
theme_tree2_internal Source code
viewClade Man page Source code
xlim_expand Man page Source code
xlim_tree Man page Source code

Files

CONTRIBUTORS.md
DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/Date.R
R/MRCA.R
R/NJ.R
R/RAxML.R
R/ape.R
R/as.polytomy.R
R/beast.R
R/clade-functions.R
R/codeml.R
R/codeml_mlc.R
R/experimental_function.R
R/facet_plot.R
R/geom_balance.R
R/geom_cladelabel.R
R/geom_hilight.R
R/geom_label.R
R/geom_point.R
R/geom_range.R
R/geom_segment.R
R/geom_strip.R
R/geom_taxalink.R
R/geom_text.R
R/geom_tiplab.R
R/geom_tree.R
R/geom_treescale.R
R/ggtree-package.R
R/ggtree.R
R/gheatmap.R
R/hyphy.R
R/inset.R
R/jplace.R
R/layout.R
R/method-drop-tip.R
R/method-fortify.R
R/method-get-tree.R
R/method-groupClade.R
R/method-groupOTU.R
R/method-gzoom.R
R/method-identify.R
R/method-print.R
R/method-reroot.R
R/method-scale-color.R
R/method-show.R
R/msaplot.R
R/multiplot.R
R/operator.R
R/paml.R
R/paml_rst.R
R/phangorn.R
R/phylip.R
R/phylopic.R
R/plot.R
R/r8s.R
R/rescale_tree.R
R/subview.R
R/theme.R
R/tidytree.R
R/treeio.R
R/utilities.R
R/xlim.R
R/zzz.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/as.phylo.igraph.R
inst/doc
inst/doc/advanceTreeAnnotation.R
inst/doc/advanceTreeAnnotation.Rmd
inst/doc/advanceTreeAnnotation.html
inst/doc/ggtree.R
inst/doc/ggtree.Rmd
inst/doc/ggtree.html
inst/doc/ggtreeUtilities.R
inst/doc/ggtreeUtilities.Rmd
inst/doc/ggtreeUtilities.html
inst/doc/treeAnnotation.R
inst/doc/treeAnnotation.Rmd
inst/doc/treeAnnotation.html
inst/doc/treeImport.R
inst/doc/treeImport.Rmd
inst/doc/treeImport.html
inst/doc/treeManipulation.R
inst/doc/treeManipulation.Rmd
inst/doc/treeManipulation.html
inst/doc/treeVisualization.R
inst/doc/treeVisualization.Rmd
inst/doc/treeVisualization.html
inst/examples
inst/examples/FluA_H3_AA.fas
inst/examples/Genotype.txt
inst/examples/MCC_FluA_H3.tree
inst/examples/NAG_inHA1.txt
inst/examples/mlc
inst/examples/rst
inst/examples/sites.txt
man
man/Date2decimal.Rd
man/GetSubtree.df.Rd
man/GetSubtreeUnrooted.Rd
man/MRCA.Rd
man/NJ.Rd
man/add-TREEDATA.Rd
man/add_TREEINFO.Rd
man/add_colorbar.Rd
man/annotation_image.Rd
man/apeBoot.Rd
man/applyLayoutDaylight.Rd
man/as.binary.Rd
man/as.data.frame.phylo.Rd
man/as.polytomy.Rd
man/collapse.Rd
man/decimal2Date.Rd
man/dotFun.Rd
man/download.phylopic.Rd
man/expand.Rd
man/facet_plot.Rd
man/flip.Rd
man/fortify.Rd
man/geom_aline.Rd
man/geom_balance.Rd
man/geom_cladelabel.Rd
man/geom_hilight.Rd
man/geom_label2.Rd
man/geom_nodepoint.Rd
man/geom_point2.Rd
man/geom_range.Rd
man/geom_rootpoint.Rd
man/geom_segment2.Rd
man/geom_strip.Rd
man/geom_taxalink.Rd
man/geom_text2.Rd
man/geom_tiplab.Rd
man/geom_tiplab2.Rd
man/geom_tippoint.Rd
man/geom_tree.Rd
man/geom_tree2.Rd
man/geom_treescale.Rd
man/get.offspring.tip.Rd
man/get.path.Rd
man/get.phylopic.Rd
man/getChild.df.Rd
man/getNodeAngle.df.Rd
man/getNodesBreadthFirst.df.Rd
man/getParent.df.Rd
man/getSubtree.Rd
man/getSubtreeUnrooted.df.Rd
man/getTreeArcAngles.Rd
man/get_balance_position.Rd
man/get_clade_position.Rd
man/get_heatmap_column_position.Rd
man/get_taxa_name.Rd
man/ggtree-ggproto.Rd
man/ggtree.Rd
man/gheatmap.Rd
man/groupClade-methods.Rd
man/groupOTU-methods.Rd
man/gzoom-methods.Rd
man/gzoom.phylo.Rd
man/identify.Rd
man/inset.Rd
man/layoutDaylight.Rd
man/layoutEqualAngle.Rd
man/msaplot.Rd
man/multiplot.Rd
man/nodebar.Rd
man/nodeid.Rd
man/nodepie.Rd
man/open_tree.Rd
man/phylopic.Rd
man/pipe.Rd
man/print.beastList.Rd
man/reroot-methods.Rd
man/rescale_tree.Rd
man/revts.Rd
man/rm.singleton.newick.Rd
man/rotate.Rd
man/rotateTreePoints.df.Rd
man/rotate_tree.Rd
man/scaleClade.Rd
man/scale_color-methods.Rd
man/scale_x_ggtree.Rd
man/stat_balance.Rd
man/stat_hilight.Rd
man/subview.Rd
man/theme_inset.Rd
man/theme_transparent.Rd
man/theme_tree.Rd
man/theme_tree2.Rd
man/update-TREE.Rd
man/viewClade.Rd
man/xlim_expand.Rd
man/xlim_tree.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-conversion.R
tests/testthat/test-geom_balance.R
tests/testthat/test-geom_cladelabel.R
tests/testthat/test-group.R
tests/testthat/test-xlim_expand.R
tests/testthat/testthat.R
vignettes
vignettes/advanceTreeAnnotation.Rmd
vignettes/figures
vignettes/figures/fan_layout.gif
vignettes/figures/ggtree_objects.png
vignettes/figures/ggtree_objects_v2.png
vignettes/figures/inset_img.png
vignettes/figures/phangorn_example.png
vignettes/figures/phylobase_example.png
vignettes/figures/phylopic1.png
vignettes/figures/phylopic2.png
vignettes/figures/rotate_clade.gif
vignettes/figures/rotate_tree.gif
vignettes/figures/subview_animation.gif
vignettes/ggtree.Rmd
vignettes/ggtree.bib
vignettes/ggtreeUtilities.Rmd
vignettes/nature.csl
vignettes/toc.css
vignettes/treeAnnotation.Rmd
vignettes/treeImport.Rmd
vignettes/treeManipulation.Rmd
vignettes/treeVisualization.Rmd
ggtree documentation built on May 20, 2017, 10:36 p.m.