1. ggtree
  2. man
  3. groupOTU-methods.Rd
Browse code

update according to treeio and tidytree

guangchuang yu authored on 11/12/2017 14:18:00
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ fcbe901f
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deleted file mode 100644
... ... 
@@ -1,22 +0,0 @@
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-% Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/method-groupOTU.R
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-\docType{methods}
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-\name{groupOTU}
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-\alias{groupOTU}
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-\alias{groupOTU,ggtree-method}
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-\title{groupOTU method}
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-\usage{
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-\S4method{groupOTU}{ggtree}(object, focus, group_name = "group", ...)
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-}
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-\arguments{
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-\item{object}{ggtree object}
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-
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-\item{focus}{OTU to focus}
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-
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-\item{group_name}{name of the group}
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-
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-\item{...}{additional parameters}
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-}
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-\description{
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-groupOTU method for ggtree object
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-}
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 363c0555
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@@ -20,4 +20,3 @@
20 20 
 \description{
21 21 
 groupOTU method for ggtree object
22 22 
 }
23 
-
Browse code

update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ f0e199ad
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@@ -20,3 +20,4 @@
20 20 
 \description{
21 21 
 groupOTU method for ggtree object
22 22 
 }
23 
+
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 353dfa09
... ... 
@@ -20,4 +20,3 @@
20 20 
 \description{
21 21 
 groupOTU method for ggtree object
22 22 
 }
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-
Browse code

treeio

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@125465 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 28/12/2016 08:15:13
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ d8a0e350
... ... 
@@ -1,74 +1,23 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/hyphy.R, R/method-groupOTU.R
2 
+% Please edit documentation in R/method-groupOTU.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
5 5 
 \alias{groupOTU}
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-\alias{groupOTU,apeBootstrap-method}
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-\alias{groupOTU,beast-method}
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-\alias{groupOTU,codeml-method}
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-\alias{groupOTU,codeml_mlc-method}
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-\alias{groupOTU,gg-method}
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-\alias{groupOTU,ggplot-method}
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-\alias{groupOTU,hyphy-method}
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-\alias{groupOTU,jplace-method}
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-\alias{groupOTU,nhx-method}
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-\alias{groupOTU,paml_rst-method}
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-\alias{groupOTU,phangorn-method}
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-\alias{groupOTU,phylip-method}
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-\alias{groupOTU,phylo-method}
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-\alias{groupOTU,r8s-method}
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-\alias{groupOTU,raxml-method}
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+\alias{groupOTU,ggtree-method}
21 7 
 \title{groupOTU method}
22 8 
 \usage{
23 
-groupOTU(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{raxml}(object, focus, group_name = "group")
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-
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-\S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
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-
29 
-\S4method{groupOTU}{apeBootstrap}(object, focus, group_name = "group", ...)
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-
31 
-\S4method{groupOTU}{beast}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{codeml}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{gg}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{ggplot}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{jplace}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{nhx}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{phangorn}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{phylip}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{phylo}(object, focus, group_name = "group", ...)
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-
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-\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE",
54 
-  ...)
9 
+\S4method{groupOTU}{ggtree}(object, focus, group_name = "group", ...)
55 10 
 }
56 11 
 \arguments{
57 
-\item{object}{supported objects, including phylo, paml_rst,
58 
-codeml_mlc, codeml, jplace, beast, hyphy}
12 
+\item{object}{ggtree object}
59 13
60 
-\item{focus}{a vector of tip (label or number) or a list of tips.}
14 
+\item{focus}{OTU to focus}
61 15
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-\item{group_name}{name of the group, 'group' by default}
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+\item{group_name}{name of the group}
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64 
-\item{...}{additional parameter}
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-
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-\item{tree}{which tree selected}
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-}
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-\value{
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-group index
18 
+\item{...}{additional parameters}
70 19 
 }
71 20 
 \description{
72 
-group tree based on selected OTU, will traceback to MRCA
21 
+groupOTU method for ggtree object
73 22 
 }
74 23
Browse code

overlap parameter in groupOTU

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@124179 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 16/11/2016 05:50:08
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 0d9e240e
... ... 
@@ -26,31 +26,32 @@ groupOTU(object, focus, group_name = "group", ...)
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 \S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
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-\S4method{groupOTU}{apeBootstrap}(object, focus, group_name = "group")
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+\S4method{groupOTU}{apeBootstrap}(object, focus, group_name = "group", ...)
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-\S4method{groupOTU}{beast}(object, focus, group_name = "group")
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+\S4method{groupOTU}{beast}(object, focus, group_name = "group", ...)
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-\S4method{groupOTU}{codeml}(object, focus, group_name = "group")
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+\S4method{groupOTU}{codeml}(object, focus, group_name = "group", ...)
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-\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
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+\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group", ...)
36 36
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-\S4method{groupOTU}{gg}(object, focus, group_name)
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+\S4method{groupOTU}{gg}(object, focus, group_name = "group", ...)
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-\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
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+\S4method{groupOTU}{ggplot}(object, focus, group_name = "group", ...)
40 40
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-\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
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+\S4method{groupOTU}{jplace}(object, focus, group_name = "group", ...)
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-\S4method{groupOTU}{nhx}(object, focus, group_name = "group")
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+\S4method{groupOTU}{nhx}(object, focus, group_name = "group", ...)
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-\S4method{groupOTU}{phangorn}(object, focus, group_name = "group")
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+\S4method{groupOTU}{phangorn}(object, focus, group_name = "group", ...)
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-\S4method{groupOTU}{phylip}(object, focus, group_name = "group")
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+\S4method{groupOTU}{phylip}(object, focus, group_name = "group", ...)
48 48
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-\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
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+\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group", ...)
50 50
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-\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
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+\S4method{groupOTU}{phylo}(object, focus, group_name = "group", ...)
52 52
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-\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
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+\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE",
54 
+  ...)
54 55 
 }
55 56 
 \arguments{
56 57 
 \item{object}{supported objects, including phylo, paml_rst,
Browse code

support phylip format

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@112578 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 15/01/2016 04:55:05
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ df059d88
... ... 
@@ -1,5 +1,5 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/hyphy.R, R/jplace.R, R/method-groupOTU.R
2 
+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/hyphy.R, R/method-groupOTU.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
5 5 
 \alias{groupOTU}
... ... 
@@ -14,6 +14,7 @@
14 14 
 \alias{groupOTU,nhx-method}
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 \alias{groupOTU,paml_rst-method}
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 \alias{groupOTU,phangorn-method}
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+\alias{groupOTU,phylip-method}
17 18 
 \alias{groupOTU,phylo-method}
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 \alias{groupOTU,r8s-method}
19 20 
 \alias{groupOTU,raxml-method}
... ... 
@@ -25,10 +26,6 @@ groupOTU(object, focus, group_name = "group", ...)
25 26
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 \S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
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-\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
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-
30 
-\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
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-
32 29 
 \S4method{groupOTU}{apeBootstrap}(object, focus, group_name = "group")
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34 31 
 \S4method{groupOTU}{beast}(object, focus, group_name = "group")
... ... 
@@ -37,17 +34,23 @@ groupOTU(object, focus, group_name = "group", ...)
37 34
38 35 
 \S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
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-\S4method{groupOTU}{nhx}(object, focus, group_name = "group")
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+\S4method{groupOTU}{gg}(object, focus, group_name)
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-\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
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+\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
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+
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+\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
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+
43 
+\S4method{groupOTU}{nhx}(object, focus, group_name = "group")
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44 45 
 \S4method{groupOTU}{phangorn}(object, focus, group_name = "group")
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-\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
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+\S4method{groupOTU}{phylip}(object, focus, group_name = "group")
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-\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
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+\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
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-\S4method{groupOTU}{gg}(object, focus, group_name)
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+\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
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+
53 
+\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
51 54 
 }
52 55 
 \arguments{
53 56 
 \item{object}{supported objects, including phylo, paml_rst,
Browse code

update ggtree with new features according to ggplot2 v2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111988 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 29/12/2015 11:53:44
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ af18d052
... ... 
@@ -1,5 +1,5 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/groupOTU.R, R/hyphy.R, R/jplace.R, R/method-groupOTU.R
2 
+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/hyphy.R, R/jplace.R, R/method-groupOTU.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
5 5 
 \alias{groupOTU}
... ... 
@@ -23,16 +23,6 @@ groupOTU(object, focus, group_name = "group", ...)
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24 24 
 \S4method{groupOTU}{raxml}(object, focus, group_name = "group")
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-\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
27 
-
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-\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
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-
30 
-\S4method{groupOTU}{codeml}(object, focus, group_name = "group")
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-
32 
-\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
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-
34 
-\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
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-
36 26 
 \S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
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38 28 
 \S4method{groupOTU}{jplace}(object, focus, group_name = "group")
... ... 
@@ -69,8 +59,6 @@ codeml_mlc, codeml, jplace, beast, hyphy}
69 59
70 60 
 \item{...}{additional parameter}
71 61
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-\item{tree}{which tree selected}
73 
-
74 62 
 \item{tree}{which tree selected}
75 63 
 }
76 64 
 \value{
Browse code

fixed typo in DESCRIPTION

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111817 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 22/12/2015 04:28:22
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 539335ec
... ... 
@@ -1,5 +1,5 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/ggtree.R, R/hyphy.R, R/jplace.R, R/method-groupOTU.R
2 
+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/groupOTU.R, R/hyphy.R, R/jplace.R, R/method-groupOTU.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
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 \alias{groupOTU}
... ... 
@@ -23,9 +23,15 @@ groupOTU(object, focus, group_name = "group", ...)
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 \S4method{groupOTU}{raxml}(object, focus, group_name = "group")
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-\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
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+\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
27 27
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-\S4method{groupOTU}{gg}(object, focus, group_name)
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+\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
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+
30 
+\S4method{groupOTU}{codeml}(object, focus, group_name = "group")
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+
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+\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
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+
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+\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
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30 36 
 \S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
31 37
... ... 
@@ -48,6 +54,10 @@ groupOTU(object, focus, group_name = "group", ...)
48 54 
 \S4method{groupOTU}{phangorn}(object, focus, group_name = "group")
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50 56 
 \S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
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+
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+\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
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+
60 
+\S4method{groupOTU}{gg}(object, focus, group_name)
51 61 
 }
52 62 
 \arguments{
53 63 
 \item{object}{supported objects, including phylo, paml_rst,
... ... 
@@ -59,6 +69,8 @@ codeml_mlc, codeml, jplace, beast, hyphy}
59 69
60 70 
 \item{...}{additional parameter}
61 71
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+\item{tree}{which tree selected}
73 
+
62 74 
 \item{tree}{which tree selected}
63 75 
 }
64 76 
 \value{
Browse code

lots updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@111813 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 22/12/2015 04:08:02
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 6c9cd355
... ... 
@@ -1,8 +1,9 @@
1 
-% Generated by roxygen2 (4.1.1): do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/beast.R, R/ggtree.R, R/groupOTU.R, R/hyphy.R, R/jplace.R
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/ggtree.R, R/hyphy.R, R/jplace.R, R/method-groupOTU.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
5 5 
 \alias{groupOTU}
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+\alias{groupOTU,apeBootstrap-method}
6 7 
 \alias{groupOTU,beast-method}
7 8 
 \alias{groupOTU,codeml-method}
8 9 
 \alias{groupOTU,codeml_mlc-method}
... ... 
@@ -10,7 +11,9 @@
10 11 
 \alias{groupOTU,ggplot-method}
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 \alias{groupOTU,hyphy-method}
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 \alias{groupOTU,jplace-method}
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+\alias{groupOTU,nhx-method}
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 \alias{groupOTU,paml_rst-method}
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+\alias{groupOTU,phangorn-method}
14 17 
 \alias{groupOTU,phylo-method}
15 18 
 \alias{groupOTU,r8s-method}
16 19 
 \alias{groupOTU,raxml-method}
... ... 
@@ -20,25 +23,31 @@ groupOTU(object, focus, group_name = "group", ...)
20 23
21 24 
 \S4method{groupOTU}{raxml}(object, focus, group_name = "group")
22 25
23 
-\S4method{groupOTU}{beast}(object, focus, group_name = "group")
24 
-
25 
-\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
26 
+\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
26 27
27 28 
 \S4method{groupOTU}{gg}(object, focus, group_name)
28 29
30 
+\S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
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+
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+\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
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+
29 34 
 \S4method{groupOTU}{phylo}(object, focus, group_name = "group")
30 35
31 
-\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
36 
+\S4method{groupOTU}{apeBootstrap}(object, focus, group_name = "group")
37 
+
38 
+\S4method{groupOTU}{beast}(object, focus, group_name = "group")
32 39
33 40 
 \S4method{groupOTU}{codeml}(object, focus, group_name = "group")
34 41
35 42 
 \S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
36 43
44 
+\S4method{groupOTU}{nhx}(object, focus, group_name = "group")
45 
+
37 46 
 \S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
38 47
39 
-\S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
48 
+\S4method{groupOTU}{phangorn}(object, focus, group_name = "group")
40 49
41 
-\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
50 
+\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
42 51 
 }
43 52 
 \arguments{
44 53 
 \item{object}{supported objects, including phylo, paml_rst,
... ... 
@@ -56,6 +65,6 @@ codeml_mlc, codeml, jplace, beast, hyphy}
56 65 
 group index
57 66 
 }
58 67 
 \description{
59 
-groupOTU method
68 
+group tree based on selected OTU, will traceback to MRCA
60 69 
 }
61 70
Browse code

add r8s and raxml support

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@109098 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 02/10/2015 06:16:16
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 341b0ee8
... ... 
@@ -1,5 +1,5 @@
1 1 
 % Generated by roxygen2 (4.1.1): do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/ggtree.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R
2 
+% Please edit documentation in R/AllGenerics.R, R/RAxML.R, R/beast.R, R/ggtree.R, R/groupOTU.R, R/hyphy.R, R/jplace.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
5 5 
 \alias{groupOTU}
... ... 
@@ -12,27 +12,33 @@
12 12 
 \alias{groupOTU,jplace-method}
13 13 
 \alias{groupOTU,paml_rst-method}
14 14 
 \alias{groupOTU,phylo-method}
15 
+\alias{groupOTU,r8s-method}
16 
+\alias{groupOTU,raxml-method}
15 17 
 \title{groupOTU method}
16 18 
 \usage{
17 
-groupOTU(object, focus, group_name = "group")
19 
+groupOTU(object, focus, group_name = "group", ...)
20 
+
21 
+\S4method{groupOTU}{raxml}(object, focus, group_name = "group")
18 22
19 23 
 \S4method{groupOTU}{beast}(object, focus, group_name = "group")
20 24
21 
-\S4method{groupOTU}{codeml}(object, focus, group_name = "group")
25 
+\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
22 26
23 
-\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
27 
+\S4method{groupOTU}{gg}(object, focus, group_name)
24 28
25 
-\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
29 
+\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
26 30
27 
-\S4method{groupOTU}{gg}(object, focus, group_name = "group")
31 
+\S4method{groupOTU}{r8s}(object, focus, group_name = "group", tree = "TREE")
28 32
29 
-\S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
33 
+\S4method{groupOTU}{codeml}(object, focus, group_name = "group")
30 34
31 
-\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
35 
+\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
32 36
33 37 
 \S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
34 38
35 
-\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
39 
+\S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
40 
+
41 
+\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
36 42 
 }
37 43 
 \arguments{
38 44 
 \item{object}{supported objects, including phylo, paml_rst,
... ... 
@@ -41,6 +47,10 @@ codeml_mlc, codeml, jplace, beast, hyphy}
41 47 
 \item{focus}{a vector of tip (label or number) or a list of tips.}
42 48
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 \item{group_name}{name of the group, 'group' by default}
50 
+
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+\item{...}{additional parameter}
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+
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+\item{tree}{which tree selected}
44 54 
 }
45 55 
 \value{
46 56 
 group index
Browse code

group_name parameter of groupOTU/groupClade and new geom_tiplab

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106964 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 01/08/2015 08:58:16
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 68c7ac99
... ... 
@@ -14,31 +14,33 @@
14 14 
 \alias{groupOTU,phylo-method}
15 15 
 \title{groupOTU method}
16 16 
 \usage{
17 
-groupOTU(object, focus)
17 
+groupOTU(object, focus, group_name = "group")
18 18
19 
-\S4method{groupOTU}{beast}(object, focus)
19 
+\S4method{groupOTU}{beast}(object, focus, group_name = "group")
20 20
21 
-\S4method{groupOTU}{codeml}(object, focus)
21 
+\S4method{groupOTU}{codeml}(object, focus, group_name = "group")
22 22
23 
-\S4method{groupOTU}{codeml_mlc}(object, focus)
23 
+\S4method{groupOTU}{codeml_mlc}(object, focus, group_name = "group")
24 24
25 
-\S4method{groupOTU}{ggplot}(object, focus)
25 
+\S4method{groupOTU}{ggplot}(object, focus, group_name = "group")
26 26
27 
-\S4method{groupOTU}{gg}(object, focus)
27 
+\S4method{groupOTU}{gg}(object, focus, group_name = "group")
28 28
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-\S4method{groupOTU}{hyphy}(object, focus)
29 
+\S4method{groupOTU}{hyphy}(object, focus, group_name = "group")
30 30
31 
-\S4method{groupOTU}{jplace}(object, focus)
31 
+\S4method{groupOTU}{jplace}(object, focus, group_name = "group")
32 32
33 
-\S4method{groupOTU}{paml_rst}(object, focus)
33 
+\S4method{groupOTU}{paml_rst}(object, focus, group_name = "group")
34 34
35 
-\S4method{groupOTU}{phylo}(object, focus)
35 
+\S4method{groupOTU}{phylo}(object, focus, group_name = "group")
36 36 
 }
37 37 
 \arguments{
38 38 
 \item{object}{supported objects, including phylo, paml_rst,
39 39 
 codeml_mlc, codeml, jplace, beast, hyphy}
40 40
41 41 
 \item{focus}{a vector of tip (label or number) or a list of tips.}
42 
+
43 
+\item{group_name}{name of the group, 'group' by default}
42 44 
 }
43 45 
 \value{
44 46 
 group index
Browse code

better geom_tree/groupClade/groupOTU implementation & annotation_clade/annotation_clade2 functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@106946 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 31/07/2015 10:15:38
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ 94bf49f9
... ... 
@@ -1,11 +1,13 @@
1 1 
 % Generated by roxygen2 (4.1.1): do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R
2 
+% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/ggtree.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
5 5 
 \alias{groupOTU}
6 6 
 \alias{groupOTU,beast-method}
7 7 
 \alias{groupOTU,codeml-method}
8 8 
 \alias{groupOTU,codeml_mlc-method}
9 
+\alias{groupOTU,gg-method}
10 
+\alias{groupOTU,ggplot-method}
9 11 
 \alias{groupOTU,hyphy-method}
10 12 
 \alias{groupOTU,jplace-method}
11 13 
 \alias{groupOTU,paml_rst-method}
... ... 
@@ -20,6 +22,10 @@ groupOTU(object, focus)
20 22
21 23 
 \S4method{groupOTU}{codeml_mlc}(object, focus)
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+\S4method{groupOTU}{ggplot}(object, focus)
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+
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+\S4method{groupOTU}{gg}(object, focus)
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+
23 29 
 \S4method{groupOTU}{hyphy}(object, focus)
24 30
25 31 
 \S4method{groupOTU}{jplace}(object, focus)
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ca17acc22b608158936b9c2790bff2f7504f38d9

add author



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103112 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 27/04/2015 03:15:40
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ b893400f
... ... 
@@ -1,4 +1,4 @@
1 
-% Generated by roxygen2 (4.1.0): do not edit by hand
1 
+% Generated by roxygen2 (4.1.1): do not edit by hand
2 2 
 % Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 3 commits.

Commit information:

Commit id: cd270be7dff4e811297283d7cd5da2826d4c60aa

update news

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-02-04 16:24:25 +0800
Author date: 2015-02-04 16:24:25 +0800

Commit id: 240a0ebc95b76ce091f0c59c95d53db841127493

gzoom methods

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-02-04 16:23:19 +0800
Author date: 2015-02-04 16:23:19 +0800

Commit id: 55f42d1fa0d7bcddc8cf8bcdcff87f887b215acf

geom_hilight

Committed by: GuangchuangYu
Author Name: GuangchuangYu
Commit date: 2015-02-04 15:54:42 +0800
Author date: 2015-02-04 15:54:42 +0800


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@99033 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 04/02/2015 08:24:48
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ cb732553
... ... 
@@ -1,5 +1,5 @@
1 1 
 % Generated by roxygen2 (4.1.0): do not edit by hand
2 
-% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/tree.R
2 
+% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R
3 3 
 \docType{methods}
4 4 
 \name{groupOTU}
5 5 
 \alias{groupOTU}
Browse code

upgrade to 0.99.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@98386 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 16/01/2015 02:39:28
Showing 1 changed files
man/groupOTU-methods.Rd
History View file @ b921de96
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,43 @@
1 
+% Generated by roxygen2 (4.1.0): do not edit by hand
2 
+% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/tree.R
3 
+\docType{methods}
4 
+\name{groupOTU}
5 
+\alias{groupOTU}
6 
+\alias{groupOTU,beast-method}
7 
+\alias{groupOTU,codeml-method}
8 
+\alias{groupOTU,codeml_mlc-method}
9 
+\alias{groupOTU,hyphy-method}
10 
+\alias{groupOTU,jplace-method}
11 
+\alias{groupOTU,paml_rst-method}
12 
+\alias{groupOTU,phylo-method}
13 
+\title{groupOTU method}
14 
+\usage{
15 
+groupOTU(object, focus)
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+
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+\S4method{groupOTU}{beast}(object, focus)
18 
+
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+\S4method{groupOTU}{codeml}(object, focus)
20 
+
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+\S4method{groupOTU}{codeml_mlc}(object, focus)
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+
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+\S4method{groupOTU}{hyphy}(object, focus)
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+
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+\S4method{groupOTU}{jplace}(object, focus)
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+
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+\S4method{groupOTU}{paml_rst}(object, focus)
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+
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+\S4method{groupOTU}{phylo}(object, focus)
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+}
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+\arguments{
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+\item{object}{supported objects, including phylo, paml_rst,
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+codeml_mlc, codeml, jplace, beast, hyphy}
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+
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+\item{focus}{a vector of tip (label or number) or a list of tips.}
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+}
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+\value{
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+group index
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+}
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+\description{
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+groupOTU method
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+}
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+