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

update man files and fixed R check

Guangchuang Yu authored on 23/03/2022 04:13:34
Showing 1 changed files
man/scaleClade.Rd
History View file @ fbeaa25d
... ... 
@@ -7,21 +7,27 @@
7 7 
 scaleClade(tree_view = NULL, node, scale = 1, vertical_only = TRUE)
8 8 
 }
9 9 
 \arguments{
10 
-\item{tree_view}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.}
10 
+\item{tree_view}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object will be used.}
11 11
12 12 
 \item{node}{internal node number to specify a clade. If NULL, using the whole tree}
13 13
14 
-\item{scale}{scale}
14 
+\item{scale}{the scale of the selected clade. The clade will be zoom in when scale > 1,
15 
+and will be zoom out when scale < 1}
15 16
16 
-\item{vertical_only}{logical. If TRUE, only vertical will be scaled.
17 
-If FALSE, the clade will be scaled vertical and horizontally.
18 
-TRUE by default.}
17 
+\item{vertical_only}{logical. If TRUE (default), only vertical will be scaled.
18 
+If FALSE, the clade will be scaled vertical and horizontally.}
19 19 
 }
20 20 
 \value{
21 21 
 tree view
22 22 
 }
23 23 
 \description{
24 
-scale clade
24 
+zoom out/in a selected clade to emphasize or de-emphasize it
25 
+}
26 
+\examples{
27 
+x <- rtree(15)
28 
+p <- ggtree(x) + geom_tiplab() +
29 
+  geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")
30 
+scaleClade(p, 24, scale = .1)
25 31 
 }
26 32 
 \author{
27 33 
 Guangchuang Yu
Browse code

update man

Guangchuang Yu authored on 30/08/2020 09:34:25
Showing 1 changed files
man/scaleClade.Rd
History View file @ 95bd0aff
... ... 
@@ -9,7 +9,7 @@ scaleClade(tree_view = NULL, node, scale = 1, vertical_only = TRUE)
9 9 
 \arguments{
10 10 
 \item{tree_view}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.}
11 11
12 
-\item{node}{internal node number}
12 
+\item{node}{internal node number to specify a clade. If NULL, using the whole tree}
13 13
14 14 
 \item{scale}{scale}
15 15
Browse code

zoomClade and geom_zoom_clade

Guangchuang Yu authored on 03/08/2020 16:21:17
Showing 1 changed files
man/scaleClade.Rd
History View file @ 764fb630
... ... 
@@ -7,9 +7,9 @@
7 7 
 scaleClade(tree_view = NULL, node, scale = 1, vertical_only = TRUE)
8 8 
 }
9 9 
 \arguments{
10 
-\item{tree_view}{tree view}
10 
+\item{tree_view}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.}
11 11
12 
-\item{node}{clade node}
12 
+\item{node}{internal node number}
13 13
14 14 
 \item{scale}{scale}
15 15
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/scaleClade.Rd
History View file @ 363c0555
... ... 
@@ -26,4 +26,3 @@ scale clade
26 26 
 \author{
27 27 
 Guangchuang Yu
28 28 
 }
29 
-
Browse code

update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
man/scaleClade.Rd
History View file @ f0e199ad
... ... 
@@ -26,3 +26,4 @@ scale clade
26 26 
 \author{
27 27 
 Guangchuang Yu
28 28 
 }
29 
+
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing 1 changed files
man/scaleClade.Rd
History View file @ 353dfa09
... ... 
@@ -26,4 +26,3 @@ scale clade
26 26 
 \author{
27 27 
 Guangchuang Yu
28 28 
 }
29 
-
Browse code

viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@112503 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 13/01/2016 07:47:55
Showing 1 changed files
man/scaleClade.Rd
History View file @ 0b5c08bd
... ... 
@@ -1,10 +1,10 @@
1 1 
 % Generated by roxygen2: do not edit by hand
2 
-% Please edit documentation in R/ggtree.R
2 
+% Please edit documentation in R/clade-functions.R
3 3 
 \name{scaleClade}
4 4 
 \alias{scaleClade}
5 5 
 \title{scaleClade}
6 6 
 \usage{
7 
-scaleClade(tree_view, node, scale = 1, vertical_only = TRUE)
7 
+scaleClade(tree_view = NULL, node, scale = 1, vertical_only = TRUE)
8 8 
 }
9 9 
 \arguments{
10 10 
 \item{tree_view}{tree view}
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/scaleClade.Rd
History View file @ 6c9cd355
... ... 
@@ -1,4 +1,4 @@
1 
-% Generated by roxygen2 (4.1.1): do not edit by hand
1 
+% Generated by roxygen2: do not edit by hand
2 2 
 % Please edit documentation in R/ggtree.R
3 3 
 \name{scaleClade}
4 4 
 \alias{scaleClade}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 71e927079cd39a6640648cb63817e21f0b2a91cc

add TODO


Commit id: c0e98b6afe6d0fd9b7bed0f92b5f909d1cb28f73

vertical_only parameter in scaleClade


Commit id: d2029e826227000f0112629b025a91e14831a79e

add apt_packages for compiling fftwtools pkg



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@104087 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 22/05/2015 03:56:57
Showing 1 changed files
man/scaleClade.Rd
History View file @ 8d5be3f5
... ... 
@@ -4,7 +4,7 @@
4 4 
 \alias{scaleClade}
5 5 
 \title{scaleClade}
6 6 
 \usage{
7 
-scaleClade(tree_view, node, scale = 1)
7 
+scaleClade(tree_view, node, scale = 1, vertical_only = TRUE)
8 8 
 }
9 9 
 \arguments{
10 10 
 \item{tree_view}{tree view}
... ... 
@@ -12,6 +12,10 @@ scaleClade(tree_view, node, scale = 1)
12 12 
 \item{node}{clade node}
13 13
14 14 
 \item{scale}{scale}
15 
+
16 
+\item{vertical_only}{logical. If TRUE, only vertical will be scaled.
17 
+If FALSE, the clade will be scaled vertical and horizontally.
18 
+TRUE by default.}
15 19 
 }
16 20 
 \value{
17 21 
 tree view
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: d69c9b83a09656294071e778f7e2248bd05b5e9b

scaleClade function to zoom in/out selected clade(s)



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103738 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 13/05/2015 04:05:11
Showing 1 changed files
man/scaleClade.Rd
History View file @ afa023c5
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,25 @@
1 
+% Generated by roxygen2 (4.1.1): do not edit by hand
2 
+% Please edit documentation in R/ggtree.R
3 
+\name{scaleClade}
4 
+\alias{scaleClade}
5 
+\title{scaleClade}
6 
+\usage{
7 
+scaleClade(tree_view, node, scale = 1)
8 
+}
9 
+\arguments{
10 
+\item{tree_view}{tree view}
11 
+
12 
+\item{node}{clade node}
13 
+
14 
+\item{scale}{scale}
15 
+}
16 
+\value{
17 
+tree view
18 
+}
19 
+\description{
20 
+scale clade
21 
+}
22 
+\author{
23 
+Guangchuang Yu
24 
+}
25 
+