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

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'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.

Author
Guangchuang Yu and Tommy Tsan-Yuk Lam
Date of publication
None
Maintainer
Guangchuang Yu <guangchuangyu@gmail.com>
License
Artistic-2.0
Version
1.6.4
URLs

View on Bioconductor

Man pages

add_colorbar
add_colorbar
add-TREEDATA
%<+%
add_TREEINFO
%+>%
annotation_image
annotation_image
apeBoot
apeBoot
apeBootstrap-class
Class "apeBootstrap" This class stores ape bootstrapping...
as.binary
as.binary
as.data.frame.phylo
as.data.frame
as.polytomy
as.polytomy
beast-class
Class "beast" This class stores information of beast output
codeml-class
Class "codeml" This class stores information of output from...
codeml_mlc-class
Class "codeml_mlc" This class stores information of mlc file...
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_text2
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
get_clade_position
get_clade_position
get.fields-methods
get.fields method
get_heatmap_column_position
get_heatmap_column_position
getNodeNum
getNodeNum
get.offspring.tip
get.offspring.tip
get.path
get.path
get.phylopic
get.phylopic
get.placements-methods
get.placements method
getRoot
getRoot
get.subs-methods
get.subs method
get_taxa_name
get_taxa_name
get.tipseq-methods
get.tipseq method
get.treeinfo-methods
get.treeinfo method
get.tree-methods
get.tree method
get.treetext-methods
get.treetext method
ggtree
visualizing phylogenetic tree and heterogenous associated...
ggtree-ggproto
StatBalance
gheatmap
gheatmap
groupClade-methods
groupClade method
groupOTU-methods
groupOTU method
groupOTU.phylo
groupOTU.phylo
gzoom-methods
gzoom method
gzoom.phylo
gzoom
hyphy-class
Class "hyphy" This class stores information of HYPHY output
identify
identify
inset
inset
jplace-class
Class "jplace" This class stores information of jplace file.
mask
mask
merge_tree
merge_tree
MRCA
MRCA
msaplot
msaplot
multiplot
multiplot
nhx-class
Class "nhx" This class stores nhx tree
NJ
NJ
nodebar
nodebar
nodeid
nodeid
nodepie
nodepie
open_tree
open_tree
paml_rst-class
Class "paml_rst" This class stores information of rst file...
phangorn-class
Class "phangorn" This class stores ancestral sequences...
phylip-class
Class "phylip" This class stores phylip tree(s)
phylopic
phylopic
phyPML
treeAnno.pml
pipe
pipe
plot-methods
plot method
pmlToSeq
pmlToSeq
print.beastList
print
r8s-class
Class "r8s" This class stores output info from r8s
raxml2nwk
raxml2nwk
raxml-class
Class "raxml" This class stores RAxML bootstrapping analysis...
read.baseml
read.baseml
read.beast
read.beast
read.codeml
read.codeml
read.codeml_mlc
read.codeml_mlc
read.hyphy
read.hyphy
read.jplace
read.jplace
read.nhx
read.nhx
read.paml_rst
read.paml_rst
read.phylip
read.phylip
read.phyloT
read.phyloT
read.r8s
read.r8s
read.raxml
read.raxml
reexports
Objects exported from other packages
reroot-methods
reroot method
rescale_tree
rescale_tree
rm.singleton.newick
rm.singleton.newick
rotate
rotate
rotate_tree
rotate_tree
rtree
generate random tree
scaleClade
scaleClade
scale_color-methods
scale_color method
scale_x_ggtree
scale_x_ggtree
show-methods
show method
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
write.jplace
write.jplace

Files in this package

ggtree/DESCRIPTION
ggtree/NAMESPACE
ggtree/NEWS
ggtree/R
ggtree/R/AllClasses.R
ggtree/R/AllGenerics.R
ggtree/R/Date.R
ggtree/R/MRCA.R
ggtree/R/NHX.R
ggtree/R/NJ.R
ggtree/R/RAxML.R
ggtree/R/ape.R
ggtree/R/as.polytomy.R
ggtree/R/beast.R
ggtree/R/clade-functions.R
ggtree/R/codeml.R
ggtree/R/codeml_mlc.R
ggtree/R/experimental_function.R
ggtree/R/facet_plot.R
ggtree/R/geom_balance.R
ggtree/R/geom_cladelabel.R
ggtree/R/geom_hilight.R
ggtree/R/geom_label.R
ggtree/R/geom_point.R
ggtree/R/geom_range.R
ggtree/R/geom_segment.R
ggtree/R/geom_strip.R
ggtree/R/geom_taxalink.R
ggtree/R/geom_text.R
ggtree/R/geom_tiplab.R
ggtree/R/geom_tree.R
ggtree/R/geom_treescale.R
ggtree/R/ggtree-package.R
ggtree/R/ggtree.R
ggtree/R/gheatmap.R
ggtree/R/hyphy.R
ggtree/R/inset.R
ggtree/R/jplace.R
ggtree/R/layout.R
ggtree/R/merge_tree.R
ggtree/R/method-fortify.R
ggtree/R/method-get-tree.R
ggtree/R/method-groupClade.R
ggtree/R/method-groupOTU.R
ggtree/R/method-gzoom.R
ggtree/R/method-identify.R
ggtree/R/method-print.R
ggtree/R/method-reroot.R
ggtree/R/method-scale-color.R
ggtree/R/method-show.R
ggtree/R/msaplot.R
ggtree/R/multiplot.R
ggtree/R/operator.R
ggtree/R/paml.R
ggtree/R/paml_rst.R
ggtree/R/phangorn.R
ggtree/R/phylip.R
ggtree/R/phyloT.R
ggtree/R/phylopic.R
ggtree/R/plot.R
ggtree/R/r8s.R
ggtree/R/raxml2nwk.R
ggtree/R/rescale_tree.R
ggtree/R/subview.R
ggtree/R/theme.R
ggtree/R/tree-utilities.R
ggtree/R/utilities.R
ggtree/R/zzz.R
ggtree/README.md
ggtree/build
ggtree/build/vignette.rds
ggtree/inst
ggtree/inst/CITATION
ggtree/inst/as.phylo.igraph.R
ggtree/inst/doc
ggtree/inst/doc/advanceTreeAnnotation.R
ggtree/inst/doc/advanceTreeAnnotation.Rmd
ggtree/inst/doc/advanceTreeAnnotation.html
ggtree/inst/doc/ggtree.R
ggtree/inst/doc/ggtree.Rmd
ggtree/inst/doc/ggtree.html
ggtree/inst/doc/ggtreeUtilities.R
ggtree/inst/doc/ggtreeUtilities.Rmd
ggtree/inst/doc/ggtreeUtilities.html
ggtree/inst/doc/treeAnnotation.R
ggtree/inst/doc/treeAnnotation.Rmd
ggtree/inst/doc/treeAnnotation.html
ggtree/inst/doc/treeImport.R
ggtree/inst/doc/treeImport.Rmd
ggtree/inst/doc/treeImport.html
ggtree/inst/doc/treeManipulation.R
ggtree/inst/doc/treeManipulation.Rmd
ggtree/inst/doc/treeManipulation.html
ggtree/inst/doc/treeVisualization.R
ggtree/inst/doc/treeVisualization.Rmd
ggtree/inst/doc/treeVisualization.html
ggtree/inst/examples
ggtree/inst/examples/FluA_H3_AA.fas
ggtree/inst/examples/Genotype.txt
ggtree/inst/examples/MCC_FluA_H3.tree
ggtree/inst/examples/NAG_inHA1.txt
ggtree/inst/examples/mlc
ggtree/inst/examples/rst
ggtree/inst/examples/sites.txt
ggtree/inst/extdata
ggtree/inst/extdata/ADH.nhx
ggtree/inst/extdata/BEAST
ggtree/inst/extdata/BEAST/beast_mcc.tree
ggtree/inst/extdata/HYPHY
ggtree/inst/extdata/HYPHY/ancseq.nex
ggtree/inst/extdata/HYPHY/labelledtree.tree
ggtree/inst/extdata/PAML_Baseml
ggtree/inst/extdata/PAML_Baseml/mlb
ggtree/inst/extdata/PAML_Baseml/rst
ggtree/inst/extdata/PAML_Codeml
ggtree/inst/extdata/PAML_Codeml/mlc
ggtree/inst/extdata/PAML_Codeml/rst
ggtree/inst/extdata/RAxML
ggtree/inst/extdata/RAxML/Dated_FluA_H3.fas
ggtree/inst/extdata/RAxML/RAxML_bestTree.H3
ggtree/inst/extdata/RAxML/RAxML_bipartitions.H3
ggtree/inst/extdata/RAxML/RAxML_bipartitionsBranchLabels.H3
ggtree/inst/extdata/RAxML/RAxML_bootstrap.H3
ggtree/inst/extdata/RAxML/RAxML_info.H3
ggtree/inst/extdata/pa.fas
ggtree/inst/extdata/pa.nwk
ggtree/inst/extdata/pa_subs.csv
ggtree/inst/extdata/r8s
ggtree/inst/extdata/r8s/H3.r8s
ggtree/inst/extdata/r8s/H3.tree
ggtree/inst/extdata/r8s/H3_r8s_output.log
ggtree/inst/extdata/sample.jplace
ggtree/inst/extdata/sample.nwk
ggtree/inst/extdata/sample.phy
ggtree/inst/extdata/twoD.tree
ggtree/man
ggtree/man/Date2decimal.Rd
ggtree/man/MRCA.Rd
ggtree/man/NJ.Rd
ggtree/man/add-TREEDATA.Rd
ggtree/man/add_TREEINFO.Rd
ggtree/man/add_colorbar.Rd
ggtree/man/annotation_image.Rd
ggtree/man/apeBoot.Rd
ggtree/man/apeBootstrap-class.Rd
ggtree/man/as.binary.Rd
ggtree/man/as.data.frame.phylo.Rd
ggtree/man/as.polytomy.Rd
ggtree/man/beast-class.Rd
ggtree/man/codeml-class.Rd
ggtree/man/codeml_mlc-class.Rd
ggtree/man/collapse.Rd
ggtree/man/decimal2Date.Rd
ggtree/man/dotFun.Rd
ggtree/man/download.phylopic.Rd
ggtree/man/expand.Rd
ggtree/man/facet_plot.Rd
ggtree/man/flip.Rd
ggtree/man/fortify.Rd
ggtree/man/geom_aline.Rd
ggtree/man/geom_balance.Rd
ggtree/man/geom_cladelabel.Rd
ggtree/man/geom_hilight.Rd
ggtree/man/geom_label2.Rd
ggtree/man/geom_nodepoint.Rd
ggtree/man/geom_point2.Rd
ggtree/man/geom_range.Rd
ggtree/man/geom_rootpoint.Rd
ggtree/man/geom_segment2.Rd
ggtree/man/geom_strip.Rd
ggtree/man/geom_taxalink.Rd
ggtree/man/geom_text2.Rd
ggtree/man/geom_tiplab.Rd
ggtree/man/geom_tiplab2.Rd
ggtree/man/geom_tippoint.Rd
ggtree/man/geom_tree.Rd
ggtree/man/geom_tree2.Rd
ggtree/man/geom_treescale.Rd
ggtree/man/get.fields-methods.Rd
ggtree/man/get.offspring.tip.Rd
ggtree/man/get.path.Rd
ggtree/man/get.phylopic.Rd
ggtree/man/get.placements-methods.Rd
ggtree/man/get.subs-methods.Rd
ggtree/man/get.tipseq-methods.Rd
ggtree/man/get.tree-methods.Rd
ggtree/man/get.treeinfo-methods.Rd
ggtree/man/get.treetext-methods.Rd
ggtree/man/getNodeNum.Rd
ggtree/man/getRoot.Rd
ggtree/man/get_balance_position.Rd
ggtree/man/get_clade_position.Rd
ggtree/man/get_heatmap_column_position.Rd
ggtree/man/get_taxa_name.Rd
ggtree/man/ggtree-ggproto.Rd
ggtree/man/ggtree.Rd
ggtree/man/gheatmap.Rd
ggtree/man/groupClade-methods.Rd
ggtree/man/groupOTU-methods.Rd
ggtree/man/groupOTU.phylo.Rd
ggtree/man/gzoom-methods.Rd
ggtree/man/gzoom.phylo.Rd
ggtree/man/hyphy-class.Rd
ggtree/man/identify.Rd
ggtree/man/inset.Rd
ggtree/man/jplace-class.Rd
ggtree/man/mask.Rd
ggtree/man/merge_tree.Rd
ggtree/man/msaplot.Rd
ggtree/man/multiplot.Rd
ggtree/man/nhx-class.Rd
ggtree/man/nodebar.Rd
ggtree/man/nodeid.Rd
ggtree/man/nodepie.Rd
ggtree/man/open_tree.Rd
ggtree/man/paml_rst-class.Rd
ggtree/man/phangorn-class.Rd
ggtree/man/phyPML.Rd
ggtree/man/phylip-class.Rd
ggtree/man/phylopic.Rd
ggtree/man/pipe.Rd
ggtree/man/plot-methods.Rd
ggtree/man/pmlToSeq.Rd
ggtree/man/print.beastList.Rd
ggtree/man/r8s-class.Rd
ggtree/man/raxml-class.Rd
ggtree/man/raxml2nwk.Rd
ggtree/man/read.baseml.Rd
ggtree/man/read.beast.Rd
ggtree/man/read.codeml.Rd
ggtree/man/read.codeml_mlc.Rd
ggtree/man/read.hyphy.Rd
ggtree/man/read.jplace.Rd
ggtree/man/read.nhx.Rd
ggtree/man/read.paml_rst.Rd
ggtree/man/read.phylip.Rd
ggtree/man/read.phyloT.Rd
ggtree/man/read.r8s.Rd
ggtree/man/read.raxml.Rd
ggtree/man/reexports.Rd
ggtree/man/reroot-methods.Rd
ggtree/man/rescale_tree.Rd
ggtree/man/rm.singleton.newick.Rd
ggtree/man/rotate.Rd
ggtree/man/rotate_tree.Rd
ggtree/man/rtree.Rd
ggtree/man/scaleClade.Rd
ggtree/man/scale_color-methods.Rd
ggtree/man/scale_x_ggtree.Rd
ggtree/man/show-methods.Rd
ggtree/man/stat_balance.Rd
ggtree/man/stat_hilight.Rd
ggtree/man/subview.Rd
ggtree/man/theme_inset.Rd
ggtree/man/theme_transparent.Rd
ggtree/man/theme_tree.Rd
ggtree/man/theme_tree2.Rd
ggtree/man/update-TREE.Rd
ggtree/man/viewClade.Rd
ggtree/man/write.jplace.Rd
ggtree/tests
ggtree/tests/testthat
ggtree/tests/testthat.R
ggtree/tests/testthat/test-conversion.R
ggtree/tests/testthat/test-geom_balance.R
ggtree/tests/testthat/test-geom_cladelabel.R
ggtree/tests/testthat/test-group.R
ggtree/tests/testthat/testthat.R
ggtree/vignettes
ggtree/vignettes/advanceTreeAnnotation.Rmd
ggtree/vignettes/figures
ggtree/vignettes/figures/fan_layout.gif
ggtree/vignettes/figures/ggtree_objects.png
ggtree/vignettes/figures/ggtree_objects_v2.png
ggtree/vignettes/figures/inset_img.png
ggtree/vignettes/figures/phangorn_example.png
ggtree/vignettes/figures/phylobase_example.png
ggtree/vignettes/figures/phylopic1.png
ggtree/vignettes/figures/phylopic2.png
ggtree/vignettes/figures/rotate_clade.gif
ggtree/vignettes/figures/rotate_tree.gif
ggtree/vignettes/figures/subview_animation.gif
ggtree/vignettes/ggtree.Rmd
ggtree/vignettes/ggtree.bib
ggtree/vignettes/ggtreeUtilities.Rmd
ggtree/vignettes/nature.csl
ggtree/vignettes/toc.css
ggtree/vignettes/treeAnnotation.Rmd
ggtree/vignettes/treeImport.Rmd
ggtree/vignettes/treeManipulation.Rmd
ggtree/vignettes/treeVisualization.Rmd