1. ggtree
  2. man
  3. fortify.Rd
Browse code

remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3)

guangchuang yu authored on 07/12/2017 07:21:58
Showing 1 changed files
man/fortify.Rd
History View file @ 6be958c5
1 1 
deleted file mode 100644
... ... 
@@ -1,35 +0,0 @@
1 
-% Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/method-fortify.R
3 
-\name{fortify.phylo}
4 
-\alias{fortify.phylo}
5 
-\title{fortify}
6 
-\usage{
7 
-\method{fortify}{phylo}(model, data, layout = "rectangular",
8 
-  ladderize = TRUE, right = FALSE, mrsd = NULL, as.Date = FALSE, ...)
9 
-}
10 
-\arguments{
11 
-\item{model}{phylo object}
12 
-
13 
-\item{data}{not use here}
14 
-
15 
-\item{layout}{layout}
16 
-
17 
-\item{ladderize}{ladderize, logical}
18 
-
19 
-\item{right}{logical}
20 
-
21 
-\item{mrsd}{most recent sampling date}
22 
-
23 
-\item{as.Date}{logical whether using Date class in time tree}
24 
-
25 
-\item{...}{additional parameter}
26 
-}
27 
-\value{
28 
-data.frame
29 
-}
30 
-\description{
31 
-fortify a phylo to data.frame
32 
-}
33 
-\author{
34 
-Yu Guangchuang
35 
-}
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/fortify.Rd
History View file @ 363c0555
... ... 
@@ -33,4 +33,3 @@ fortify a phylo to data.frame
33 33 
 \author{
34 34 
 Yu Guangchuang
35 35 
 }
36 
-
Browse code

update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
man/fortify.Rd
History View file @ f0e199ad
... ... 
@@ -33,3 +33,4 @@ fortify a phylo to data.frame
33 33 
 \author{
34 34 
 Yu Guangchuang
35 35 
 }
36 
+
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing 1 changed files
man/fortify.Rd
History View file @ 353dfa09
... ... 
@@ -33,4 +33,3 @@ fortify a phylo to data.frame
33 33 
 \author{
34 34 
 Yu Guangchuang
35 35 
 }
36 
-
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/fortify.Rd
History View file @ 6c9cd355
... ... 
@@ -1,5 +1,5 @@
1 
-% Generated by roxygen2 (4.1.1): do not edit by hand
2 
-% Please edit documentation in R/treeIO.R
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/method-fortify.R
3 3 
 \name{fortify.phylo}
4 4 
 \alias{fortify.phylo}
5 5 
 \title{fortify}
... ... 
@@ -28,7 +28,7 @@
28 28 
 data.frame
29 29 
 }
30 30 
 \description{
31 
-fortify
31 
+fortify a phylo to data.frame
32 32 
 }
33 33 
 \author{
34 34 
 Yu Guangchuang
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/fortify.Rd
History View file @ 341b0ee8
... ... 
@@ -5,7 +5,7 @@
5 5 
 \title{fortify}
6 6 
 \usage{
7 7 
 \method{fortify}{phylo}(model, data, layout = "rectangular",
8 
-  ladderize = TRUE, right = FALSE, ...)
8 
+  ladderize = TRUE, right = FALSE, mrsd = NULL, as.Date = FALSE, ...)
9 9 
 }
10 10 
 \arguments{
11 11 
 \item{model}{phylo object}
... ... 
@@ -18,6 +18,10 @@
18 18
19 19 
 \item{right}{logical}
20 20
21 
+\item{mrsd}{most recent sampling date}
22 
+
23 
+\item{as.Date}{logical whether using Date class in time tree}
24 
+
21 25 
 \item{...}{additional parameter}
22 26 
 }
23 27 
 \value{
Browse code

update according to changes of ggplot2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107869 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 28/08/2015 13:39:22
Showing 1 changed files
man/fortify.Rd
History View file @ 1d4d6914
... ... 
@@ -4,8 +4,8 @@
4 4 
 \alias{fortify.phylo}
5 5 
 \title{fortify}
6 6 
 \usage{
7 
-\method{fortify}{phylo}(model, data, layout = "phylogram", ladderize = TRUE,
8 
-  right = FALSE, ...)
7 
+\method{fortify}{phylo}(model, data, layout = "rectangular",
8 
+  ladderize = TRUE, right = FALSE, ...)
9 9 
 }
10 10 
 \arguments{
11 11 
 \item{model}{phylo object}
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/fortify.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/treeIO.R
3 3 
 \name{fortify.phylo}
4 4 
 \alias{fortify.phylo}
Browse code

Adds ggtree/ seq2pathway/ sidap/ to the repos.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@98340 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 14/01/2015 21:22:07
Showing 1 changed files
man/fortify.Rd
History View file @ 0c8aaf33
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,32 @@
1 
+% Generated by roxygen2 (4.1.0): do not edit by hand
2 
+% Please edit documentation in R/treeIO.R
3 
+\name{fortify.phylo}
4 
+\alias{fortify.phylo}
5 
+\title{fortify}
6 
+\usage{
7 
+\method{fortify}{phylo}(model, data, layout = "phylogram", ladderize = TRUE,
8 
+  right = FALSE, ...)
9 
+}
10 
+\arguments{
11 
+\item{model}{phylo object}
12 
+
13 
+\item{data}{not use here}
14 
+
15 
+\item{layout}{layout}
16 
+
17 
+\item{ladderize}{ladderize, logical}
18 
+
19 
+\item{right}{logical}
20 
+
21 
+\item{...}{additional parameter}
22 
+}
23 
+\value{
24 
+data.frame
25 
+}
26 
+\description{
27 
+fortify
28 
+}
29 
+\author{
30 
+Yu Guangchuang
31 
+}
32 
+