1. ggtree
  2. man
  3. geom_tippoint.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/geom_tippoint.Rd
History View file @ fbeaa25d
... ... 
@@ -20,16 +20,16 @@ If \code{inherit.aes = TRUE}, the mapping can be inherited from the plot mapping
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 specified in the call to \code{ggplot()}.}
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 \item{data}{The data to be displayed in this layer. If 'NULL' (the default),
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-the data is inherited from the plot data as specified in the call to 'ggplot()',}
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+the data is inherited from the plot data as specified in the call to \code{ggplot()}.}
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 \item{position}{Position adjustment.}
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-\item{na.rm}{logical. If 'FALSE' (the default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.}
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+\item{na.rm}{logical. If 'FALSE' (default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.}
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 \item{show.legend}{logical. Should this layer be included in the legends?
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 'NA', the default, includes if any aesthetics are mapped. 'FALSE' never includes, and 'TRUE' always includes.}
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-\item{inherit.aes}{logical (default is 'TRUE'). If 'FALSE', overrides the default aesthetics,
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+\item{inherit.aes}{logical (defaults to 'TRUE'). If 'FALSE', overrides the default aesthetics,
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 rather then combining with them.}
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 \item{...}{addtional parameters that passed on to this layer. These are often aesthetics, used to set an aesthetic to a fixed value, like \code{colour = "red"} or \code{size = 3}.}
... ... 
@@ -38,7 +38,18 @@ rather then combining with them.}
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 tip point layer
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 }
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 \description{
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-add tip point
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+add tip point layer for a tree
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+}
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+\examples{
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+library(ggtree)
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+tr<- rtree(15)
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+x <- ggtree(tr)
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+x + geom_tippoint()
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+}
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+\references{
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+For more detailed demonstration, please refer to chapter 4.3.2 of
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+\emph{Data Integration, Manipulation and Visualization of Phylogenetic Trees}
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+\url{http://yulab-smu.top/treedata-book/index.html} by Guangchuang Yu.
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 }
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 \author{
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 Guangchuang Yu
Browse code

update geom_point2 manual

Guangchuang Yu authored on 25/08/2020 03:22:29
Showing 1 changed files
man/geom_tippoint.Rd
History View file @ 70402823
... ... 
@@ -15,19 +15,24 @@ geom_tippoint(
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 )
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 }
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 \arguments{
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-\item{mapping}{aes mapping}
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+\item{mapping}{Set of aesthetic mapping created by \code{aes()}.
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+If \code{inherit.aes = TRUE}, the mapping can be inherited from the plot mapping as
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+specified in the call to \code{ggplot()}.}
19 21
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-\item{data}{data}
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+\item{data}{The data to be displayed in this layer. If 'NULL' (the default),
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+the data is inherited from the plot data as specified in the call to 'ggplot()',}
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-\item{position}{position}
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+\item{position}{Position adjustment.}
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-\item{na.rm}{logical}
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+\item{na.rm}{logical. If 'FALSE' (the default), missing values are removed with a warning. If 'TRUE', missing values are silently removed.}
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-\item{show.legend}{logical}
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+\item{show.legend}{logical. Should this layer be included in the legends?
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+'NA', the default, includes if any aesthetics are mapped. 'FALSE' never includes, and 'TRUE' always includes.}
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-\item{inherit.aes}{logical}
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+\item{inherit.aes}{logical (default is 'TRUE'). If 'FALSE', overrides the default aesthetics,
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+rather then combining with them.}
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-\item{...}{addktional parameter}
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+\item{...}{addtional parameters that passed on to this layer. These are often aesthetics, used to set an aesthetic to a fixed value, like \code{colour = "red"} or \code{size = 3}.}
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 }
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 \value{
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 tip point layer
Browse code

clip="off" and update docs

Guangchuang Yu authored on 06/12/2019 03:01:17
Showing 1 changed files
man/geom_tippoint.Rd
History View file @ fb0a330e
... ... 
@@ -4,8 +4,15 @@
4 4 
 \alias{geom_tippoint}
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 \title{geom_tippoint}
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 \usage{
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-geom_tippoint(mapping = NULL, data = NULL, position = "identity",
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-  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
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+geom_tippoint(
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+  mapping = NULL,
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+  data = NULL,
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+  position = "identity",
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+  na.rm = FALSE,
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+  show.legend = NA,
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+  inherit.aes = TRUE,
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+  ...
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+)
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 }
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 \arguments{
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 \item{mapping}{aes mapping}
Browse code

geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/geom_tippoint.Rd
History View file @ 363c0555
... ... 
@@ -31,4 +31,3 @@ add tip point
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 \author{
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 Guangchuang Yu
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 }
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-
Browse code

update docs

guangchuang yu authored on 16/08/2017 02:36:13
Showing 1 changed files
man/geom_tippoint.Rd
History View file @ f0e199ad
... ... 
@@ -31,3 +31,4 @@ add tip point
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 \author{
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 Guangchuang Yu
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 }
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+
Browse code

add extend parameter in geom_cladelabel

guangchuang yu authored on 26/07/2017 02:13:53
Showing 1 changed files
man/geom_tippoint.Rd
History View file @ 353dfa09
... ... 
@@ -31,4 +31,3 @@ add tip point
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 \author{
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 Guangchuang Yu
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 }
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-
Browse code

geom_label2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@115937 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 07/04/2016 04:02:44
Showing 1 changed files
man/geom_tippoint.Rd
History View file @ 7d9641c6
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@@ -4,17 +4,14 @@
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 \alias{geom_tippoint}
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 \title{geom_tippoint}
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 \usage{
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-geom_tippoint(mapping = NULL, data = NULL, stat = "identity",
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-  position = "identity", na.rm = FALSE, show.legend = NA,
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-  inherit.aes = TRUE, ...)
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+geom_tippoint(mapping = NULL, data = NULL, position = "identity",
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+  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
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 }
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 \arguments{
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 \item{mapping}{aes mapping}
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 \item{data}{data}
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-\item{stat}{stat}
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-
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 \item{position}{position}
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 \item{na.rm}{logical}
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
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man/geom_tippoint.Rd
History View file @ 6c9cd355
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@@ -1,15 +1,29 @@
1 
-% 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/geom_point.R
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 \name{geom_tippoint}
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 \alias{geom_tippoint}
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 \title{geom_tippoint}
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 \usage{
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-geom_tippoint(mapping = NULL, ...)
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+geom_tippoint(mapping = NULL, data = NULL, stat = "identity",
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+  position = "identity", na.rm = FALSE, show.legend = NA,
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+  inherit.aes = TRUE, ...)
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 }
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 \arguments{
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 \item{mapping}{aes mapping}
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-\item{...}{additional parameter}
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+\item{data}{data}
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+
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+\item{stat}{stat}
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+
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+\item{position}{position}
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+
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+\item{na.rm}{logical}
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+
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+\item{show.legend}{logical}
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+
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+\item{inherit.aes}{logical}
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+
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+\item{...}{addktional parameter}
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 }
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 \value{
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 tip point layer
Browse code

revert to previous version for compatible with CRAN version of ggplot2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@107950 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 31/08/2015 03:34:32
Showing 1 changed files
man/geom_tippoint.Rd
History View file @ 8d490ae5
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@@ -4,26 +4,12 @@
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 \alias{geom_tippoint}
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 \title{geom_tippoint}
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 \usage{
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-geom_tippoint(mapping = NULL, data = NULL, stat = "identity",
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-  position = "identity", na.rm = FALSE, show.legend = NA,
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-  inherit.aes = TRUE, ...)
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+geom_tippoint(mapping = NULL, ...)
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 }
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 \arguments{
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 \item{mapping}{aes mapping}
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-\item{data}{data}
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-
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-\item{stat}{stat}
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-
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-\item{position}{position}
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-
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-\item{na.rm}{logical}
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-
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-\item{show.legend}{logical}
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-
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-\item{inherit.aes}{logical}
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-
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-\item{...}{addktional parameter}
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+\item{...}{additional parameter}
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 }
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 \value{
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 tip point layer
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/geom_tippoint.Rd
History View file @ 1d4d6914
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@@ -1,26 +1,37 @@
1 1 
 % 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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+% Please edit documentation in R/geom_point.R
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 \name{geom_tippoint}
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 \alias{geom_tippoint}
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 \title{geom_tippoint}
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 \usage{
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-geom_tippoint(...)
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+geom_tippoint(mapping = NULL, data = NULL, stat = "identity",
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+  position = "identity", na.rm = FALSE, show.legend = NA,
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+  inherit.aes = TRUE, ...)
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 }
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 \arguments{
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-\item{...}{additional parameter}
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+\item{mapping}{aes mapping}
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+
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+\item{data}{data}
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+
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+\item{stat}{stat}
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+
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+\item{position}{position}
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+
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+\item{na.rm}{logical}
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+
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+\item{show.legend}{logical}
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+
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+\item{inherit.aes}{logical}
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+
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+\item{...}{addktional parameter}
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 }
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 \value{
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 tip point layer
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 }
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 \description{
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-add points layer of tips
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-}
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-\examples{
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-require(ape)
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-tr <- rtree(10)
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-ggtree(tr) + geom_tippoint()
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+add tip point
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 }
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 \author{
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-Yu Guangchuang
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+Guangchuang Yu
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 }
26 37
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/geom_tippoint.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
2 2 
 % Please edit documentation in R/ggtree.R
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 \name{geom_tippoint}
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 \alias{geom_tippoint}
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/geom_tippoint.Rd
History View file @ 0c8aaf33
1 1 
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{geom_tippoint}
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+\alias{geom_tippoint}
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+\title{geom_tippoint}
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+\usage{
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+geom_tippoint(...)
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+}
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+\arguments{
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+\item{...}{additional parameter}
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+}
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+\value{
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+tip point layer
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+}
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+\description{
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+add points layer of tips
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+}
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+\examples{
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+require(ape)
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+tr <- rtree(10)
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+ggtree(tr) + geom_tippoint()
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+}
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+\author{
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+Yu Guangchuang
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+}
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+