1. ggtree
  2. man
  3. collapse.Rd
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update man files and fixed R check

Guangchuang Yu authored on 23/03/2022 04:13:34
Showing 1 changed files
man/collapse.Rd
History View file @ fbeaa25d
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@@ -11,17 +11,24 @@
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 \item{node}{internal node number}
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-\item{mode}{one of 'none', 'max', 'min' and 'mixed'}
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+\item{mode}{one of 'none'(default), 'max', 'min' and 'mixed'. 'none' would simply collapse the clade as 'tip' and
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+the rest will display a triangle, whose shape is determined by the farest/closest tip of the collapsed clade to indicate it}
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-\item{clade_name}{set clade name. If clade_name = NULL, do nothing}
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+\item{clade_name}{set a name for the collapsed clade. If clade_name = NULL, do nothing}
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-\item{...}{additional parameters}
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+\item{...}{additional parameters to set the color or transparency of the triangle}
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 }
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 \value{
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 tree view
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 }
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 \description{
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-collapse a clade
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+collapse a selected clade, which can later be expanded with the 'expand()' fuction if necessary
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+}
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+\examples{
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+x <- rtree(15)
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+p <- ggtree(x) + geom_tiplab()
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+p
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+p1 <- collapse(p, node = 17, mode = "mixed", clade_name = "cclade", alpha = 0.8, color = "grey", fill = "light blue")
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 }
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 \seealso{
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 expand
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zoomClade and geom_zoom_clade

Guangchuang Yu authored on 03/08/2020 16:21:17
Showing 1 changed files
man/collapse.Rd
History View file @ 764fb630
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@@ -7,9 +7,9 @@
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 \method{collapse}{ggtree}(x = NULL, node, mode = "none", clade_name = NULL, ...)
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 }
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 \arguments{
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-\item{x}{tree view}
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+\item{x}{tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.}
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-\item{node}{clade node}
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+\item{node}{internal node number}
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 \item{mode}{one of 'none', 'max', 'min' and 'mixed'}
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clip="off" and update docs

Guangchuang Yu authored on 06/12/2019 03:01:17
Showing 1 changed files
man/collapse.Rd
History View file @ fb0a330e
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@@ -4,8 +4,7 @@
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 \alias{collapse.ggtree}
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 \title{collapse-ggtree}
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 \usage{
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-\method{collapse}{ggtree}(x = NULL, node, mode = "none",
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-  clade_name = NULL, ...)
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+\method{collapse}{ggtree}(x = NULL, node, mode = "none", clade_name = NULL, ...)
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 }
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 \arguments{
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 \item{x}{tree view}
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mode paramter in collapse

Guangchuang Yu authored on 11/07/2019 05:43:27
Showing 1 changed files
man/collapse.Rd
History View file @ 7f09bee0
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@@ -4,13 +4,16 @@
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 \alias{collapse.ggtree}
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 \title{collapse-ggtree}
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 \usage{
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-\method{collapse}{ggtree}(x = NULL, node, clade_name = NULL, ...)
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+\method{collapse}{ggtree}(x = NULL, node, mode = "none",
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+  clade_name = NULL, ...)
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 }
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 \arguments{
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 \item{x}{tree view}
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 \item{node}{clade node}
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+\item{mode}{one of 'none', 'max', 'min' and 'mixed'}
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+
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 \item{clade_name}{set clade name. If clade_name = NULL, do nothing}
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 \item{...}{additional parameters}
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clade_name paramter in collapse

guangchuang yu authored on 28/05/2018 03:02:54
Showing 1 changed files
man/collapse.Rd
History View file @ 591825ec
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@@ -4,13 +4,15 @@
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 \alias{collapse.ggtree}
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 \title{collapse-ggtree}
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 \usage{
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-\method{collapse}{ggtree}(x = NULL, node, ...)
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+\method{collapse}{ggtree}(x = NULL, node, clade_name = NULL, ...)
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 }
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 \arguments{
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 \item{x}{tree view}
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 \item{node}{clade node}
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+\item{clade_name}{set clade name. If clade_name = NULL, do nothing}
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+
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 \item{...}{additional parameters}
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 }
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 \value{
Browse code

update vignettes

guangchuang yu authored on 03/01/2018 09:55:53
Showing 1 changed files
man/collapse.Rd
History View file @ 0266c285
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@@ -1,15 +1,17 @@
1 1 
 % Generated by roxygen2: do not edit by hand
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 % Please edit documentation in R/clade-functions.R
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-\name{collapse}
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-\alias{collapse}
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-\title{collapse}
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+\name{collapse.ggtree}
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+\alias{collapse.ggtree}
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+\title{collapse-ggtree}
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 \usage{
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-collapse(tree_view = NULL, node)
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+\method{collapse}{ggtree}(x = NULL, node, ...)
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 }
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 \arguments{
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-\item{tree_view}{tree view}
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+\item{x}{tree view}
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 \item{node}{clade node}
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+
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+\item{...}{additional parameters}
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 }
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 \value{
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 tree view
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/collapse.Rd
History View file @ 363c0555
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@@ -17,10 +17,9 @@ tree view
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 \description{
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 collapse a clade
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 }
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-\author{
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-Guangchuang Yu
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-}
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 \seealso{
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 expand
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 }
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-
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+\author{
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+Guangchuang Yu
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+}
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update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
man/collapse.Rd
History View file @ f0e199ad
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@@ -17,9 +17,10 @@ tree view
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 \description{
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 collapse a clade
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 }
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-\seealso{
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-expand
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\seealso{
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+expand
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+}
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+
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add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing 1 changed files
man/collapse.Rd
History View file @ 353dfa09
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@@ -17,10 +17,9 @@ tree view
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 \description{
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 collapse a clade
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 }
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-\author{
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-Guangchuang Yu
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-}
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 \seealso{
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 expand
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 }
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-
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+\author{
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+Guangchuang Yu
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+}
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/collapse.Rd
History View file @ 0b5c08bd
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@@ -1,10 +1,10 @@
1 1 
 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/ggtree.R
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+% Please edit documentation in R/clade-functions.R
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 \name{collapse}
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 \alias{collapse}
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 \title{collapse}
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 \usage{
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-collapse(tree_view, node)
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+collapse(tree_view = NULL, node)
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 }
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 \arguments{
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 \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/collapse.Rd
History View file @ 6c9cd355
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@@ -1,4 +1,4 @@
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-% Generated by roxygen2 (4.1.1): do not edit by hand
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+% Generated by roxygen2: do not edit by hand
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 % Please edit documentation in R/ggtree.R
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 \name{collapse}
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 \alias{collapse}
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/collapse.Rd
History View file @ b893400f
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@@ -1,4 +1,4 @@
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-% Generated by roxygen2 (4.1.0): do not edit by hand
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+% Generated by roxygen2 (4.1.1): do not edit by hand
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 % Please edit documentation in R/ggtree.R
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 \name{collapse}
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 \alias{collapse}
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: 06148bb3ff7d69f510bc9c3755ea80810415ad11

groupClade



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@100622 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 13/03/2015 04:11:52
Showing 1 changed files
man/collapse.Rd
History View file @ db1e112f
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new file mode 100644
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@@ -0,0 +1,26 @@
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+% Generated by roxygen2 (4.1.0): do not edit by hand
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+% Please edit documentation in R/ggtree.R
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+\name{collapse}
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+\alias{collapse}
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+\title{collapse}
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+\usage{
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+collapse(tree_view, node)
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+}
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+\arguments{
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+\item{tree_view}{tree view}
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+
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+\item{node}{clade node}
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+}
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+\value{
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+tree view
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+}
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+\description{
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+collapse a clade
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+}
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+\author{
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+Guangchuang Yu
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+}
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+\seealso{
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+expand
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+}
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+