A B C D E F G H I J M N O P R S T V W misc
ggtree-package | visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics 'ggtree' provides functions for visualizing phylogenetic tree and its associated data in R. |
add_colorbar | add_colorbar |
annotation_image | annotation_image |
apeBoot | apeBoot |
apeBootstrap-class | Class "apeBootstrap" This class stores ape bootstrapping analysis result |
as.binary | as.binary |
as.binary.phylo | as.binary |
as.data.frame.phylo | as.data.frame |
beast-class | Class "beast" This class stores information of beast output |
codeml-class | Class "codeml" This class stores information of output from codeml |
codeml_mlc-class | Class "codeml_mlc" This class stores information of mlc file frm codeml output |
collapse | collapse |
Date2decimal | Date2decimal |
decimal2Date | decimal2Date |
download.phylopic | download.phylopic |
expand | expand |
flip | flip |
fortify.phylo | 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.fields | get.fields method |
get.fields-method | get.fields method |
get.fields-method | Class "jplace" This class stores information of jplace file. |
get.offspring.tip | get.offspring.tip |
get.path | get.path |
get.phylopic | get.phylopic |
get.placements | get.placements method |
get.placements-method | get.placements method |
get.placements-method | Class "jplace" This class stores information of jplace file. |
get.subs | get.subs method |
get.subs-method | get.subs method |
get.tipseq | get.tipseq method |
get.tipseq-method | get.tipseq method |
get.tree | get.tree method |
get.tree,beast | get.tree method |
get.tree-method | Class "beast" This class stores information of beast output |
get.tree-method | get.tree method |
get.treeinfo | get.treeinfo method |
get.treeinfo-method | get.treeinfo method |
get.treeinfo-method | Class "jplace" This class stores information of jplace file. |
get.treetext | get.treetext method |
get.treetext-method | get.treetext method |
get.treetext-method | Class "jplace" This class stores information of jplace file. |
getNodeNum | getNodeNum |
getRoot | getRoot |
get_balance_position | get_balance_position |
get_clade_position | get_clade_position |
get_heatmap_column_position | get_heatmap_column_position |
get_taxa_name | get_taxa_name |
ggtree | visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics 'ggtree' provides functions for visualizing phylogenetic tree and its associated data in R. |
gheatmap | gheatmap |
groupClade | groupClade method |
groupClade-method | groupClade method |
groupOTU | groupOTU method |
groupOTU-method | groupOTU method |
groupOTU.phylo | groupOTU.phylo |
gzoom | gzoom method |
gzoom-method | gzoom method |
gzoom.phylo | gzoom |
hyphy-class | Class "hyphy" This class stores information of HYPHY output |
identify.gg | 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 |
package-ggtree | visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics 'ggtree' provides functions for visualizing phylogenetic tree and its associated data in R. |
paml_rst-class | Class "paml_rst" This class stores information of rst file from PAML output |
phangorn-class | Class "phangorn" This class stores ancestral sequences inferred from 'phangorn' |
phylip-class | Class "phylip" This class stores phylip tree(s) |
phylopic | phylopic |
phyPML | treeAnno.pml |
plot | plot method |
plot-method | plot method |
pmlToSeq | pmlToSeq |
print.beastList |
r8s-class | Class "r8s" This class stores output info from r8s |
raxml-class | Class "raxml" This class stores RAxML bootstrapping analysis result |
raxml2nwk | raxml2nwk |
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.r8s | read.r8s |
read.raxml | read.raxml |
reroot | reroot method |
reroot-method | 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 | scale_color method |
scale_color-method | scale_color method |
scale_x_ggtree | scale_x_ggtree |
set.subs-method | Class "paml_rst" This class stores information of rst file from PAML output |
set.subs<--method | Class "paml_rst" This class stores information of rst file from PAML output |
show | show method |
show-method | Class "jplace" This class stores information of jplace file. |
show-method | show method |
StatBalance | StatBalance |
StatHilight | StatBalance |
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 |
viewClade | viewClade |
write.jplace | write.jplace |
%<% | %<% |
%<+% | %<+% |
%>% | pipe |
. | . |