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

Global functions
. Man page
Date2decimal Man page Source code
GeomHilight Man page
MRCA 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
aes Man page
annotation_image Man page Source code
applyLayoutDaylight Man page 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
collapse.ggtree Man page Source code
color_scale Source code
coplot Source code
decimal2Date Man page Source code
draw_key_hack Source code
euc.dist Source code
expand Man page Source code
facet_plot Man page Source code
flip Man page Source code
fortify Man page
fortify.multiPhylo Source code
fortify.obkData Source code
fortify.phylo Source code
fortify.phylo4 Source code
fortify.phylo4d Source code
fortify.phyloseq 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_cladelabel2 Man page Source code
geom_hilight Man page Source code
geom_hilight_encircle Man page Source code
geom_label Man page
geom_label2 Man page Source code
geom_motif Man page Source code
geom_nodelab Man page Source code
geom_nodepoint Man page Source code
geom_point Man page
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_text Man page
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_tree Man page Source code
geom_tree2 Man page Source code
geom_treescale Man page 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.trunk 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
getNodeAngle.vector Source code
getNodeEuclDistances 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
getSubtree.df Man page Source code
getSubtreeUnrooted Man page Source code
getSubtreeUnrooted.df Man page Source code
getTreeArcAngles Man page 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_cladelabel2_position_ Source code
get_cladelabel2_position_bar Source code
get_cladelabel2_position_label Source code
get_cladelabel_position Source code
get_cladelabel_position_ Source code
get_color_attribute Source code
get_glob_encircle 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_tree_view Source code
get_treescale_position Source code
ggpie Source code
ggplot Man page
ggsave Man page
ggtree Man page Man page Source code
ggtree-package Man page
gheatmap Man page Source code
groupClade Man page
groupClade.ggtree Source code
groupOTU Man page
groupOTU.ggtree Source code
gzoom Man page Man page
gzoom,ggtree-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_attribute Source code
is.tree_attribute_ Source code
is.viewClade 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
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
range_format Man page Source code
range_lower Source code
range_upper Source code
re_assign_ycoord_df Source code
read.astral Man page
read.beast Man page
read.codeml Man page
read.codeml_mlc Man page
read.hyphy Man page
read.iqtree Man page
read.jplace Man page
read.jtree Man page
read.mrbayes Man page
read.newick Man page
read.nexus Man page
read.nhx Man page
read.paml_rst Man page
read.phylip Man page
read.phyloT Man page
read.r8s Man page
read.raxml Man page
read.tree Man page
reassign_y_from_node_to_root Source code
reexports Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page
reroot 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
rotate Man page Source code
rotateTreePoints.df Man page Source code
rotate_tree Man page Source code
roundDigit Source code
rtree Man page
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,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
set_branch_length_cladogram Source code
set_hilight_legend Man page Source code
setup_tree_data Source code
stat_balance Man page Source code
stat_cladeBar Source code
stat_cladeBar2 Source code
stat_cladeText Source code
stat_cladeText2 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
taxa2node Source code
theme Man page
theme_inset 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 Man page
xlim_expand Man page Source code
xlim_tree Man page Source code
GuangchuangYu/ggtree documentation built on April 18, 2018, 7:06 a.m.