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

geom_highlight

Guangchuang Yu authored on 08/01/2020 02:55:39
Showing 1 changed files
man/geom_hilight.Rd
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deleted file mode 100644
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-% Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/geom_hilight.R
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-\name{geom_hilight}
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-\alias{geom_hilight}
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-\title{geom_hilight}
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-\usage{
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-geom_hilight(node, fill = "steelblue", alpha = 0.5, extend = 0, ...)
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-}
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-\arguments{
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-\item{node}{selected node to hilight (required)}
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-
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-\item{fill}{color fill (default = steelblue)}
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-
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-\item{alpha}{alpha transparency, (default = 0.5)}
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-
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-\item{extend}{extend xmax of the rectangle (default = 0)}
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-
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-\item{...}{additional parameters}
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-}
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-\value{
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-ggplot2
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-}
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-\description{
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-layer of hilight clade with rectangle
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-}
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-\author{
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-Guangchuang Yu
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-}
Browse code

geom-hilight

Guangchuang Yu authored on 28/08/2019 08:27:43
Showing 1 changed files
man/geom_hilight.Rd
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@@ -4,8 +4,7 @@
4 4 
 \alias{geom_hilight}
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 \title{geom_hilight}
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 \usage{
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-geom_hilight(node, fill = "steelblue", alpha = 0.5, extend = 0,
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-  extendto = NULL)
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+geom_hilight(node, fill = "steelblue", alpha = 0.5, extend = 0, ...)
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 }
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 \arguments{
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 \item{node}{selected node to hilight (required)}
... ... 
@@ -16,7 +15,7 @@ geom_hilight(node, fill = "steelblue", alpha = 0.5, extend = 0,
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 \item{extend}{extend xmax of the rectangle (default = 0)}
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-\item{extendto}{extend xmax to extendto (default = NULL)}
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+\item{...}{additional parameters}
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 }
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 \value{
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 ggplot2
Browse code

Added revised geom_hilight_encircle() function to highlight clades of unrooted trees.

Fixed layoutDaylight ave_change calculation.

Fixed bug in getTreeArcAngles() for cases where the branch root node and origin node are the same.

Added getNodeEuclDistances() function.

Fixed isTip() function to check if nodes has children, instead of checking of the data variable had the isTip field set.

JustGitting authored on 29/06/2017 03:43:04
Showing 1 changed files
man/geom_hilight.Rd
History View file @ 9a1c4d17
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@@ -8,15 +8,15 @@ geom_hilight(node, fill = "steelblue", alpha = 0.5, extend = 0,
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   extendto = NULL)
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 }
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 \arguments{
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-\item{node}{selected node to hilight}
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+\item{node}{selected node to hilight (required)}
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-\item{fill}{color fill}
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+\item{fill}{color fill (default = steelblue)}
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-\item{alpha}{alpha (transparency)}
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+\item{alpha}{alpha transparency, (default = 0.5)}
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-\item{extend}{extend xmax of the rectangle}
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+\item{extend}{extend xmax of the rectangle (default = 0)}
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-\item{extendto}{extend xmax to extendto}
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+\item{extendto}{extend xmax to extendto (default = NULL)}
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 }
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 \value{
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 ggplot2
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@@ -27,4 +27,3 @@ layer of hilight clade with rectangle
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 \author{
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 Guangchuang Yu
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 }
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-
Browse code

update geom_hilight

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@117273 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 10/05/2016 10:16:07
Showing 1 changed files
man/geom_hilight.Rd
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@@ -4,7 +4,8 @@
4 4 
 \alias{geom_hilight}
5 5 
 \title{geom_hilight}
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 \usage{
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-geom_hilight(node, fill = "steelblue", alpha = 0.5)
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+geom_hilight(node, fill = "steelblue", alpha = 0.5, extend = 0,
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+  extendto = NULL)
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 }
9 10 
 \arguments{
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 \item{node}{selected node to hilight}
... ... 
@@ -12,6 +13,10 @@ geom_hilight(node, fill = "steelblue", alpha = 0.5)
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 \item{fill}{color fill}
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 \item{alpha}{alpha (transparency)}
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+
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+\item{extend}{extend xmax of the rectangle}
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+
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+\item{extendto}{extend xmax to extendto}
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 }
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 \value{
17 22 
 ggplot2
Browse code

update ggtree with new features according to ggplot2 v2

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

g.yu authored on 29/12/2015 11:53:44
Showing 1 changed files
man/geom_hilight.Rd
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@@ -2,14 +2,9 @@
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 % Please edit documentation in R/geom_hilight.R
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 \name{geom_hilight}
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 \alias{geom_hilight}
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-\alias{stat_hilight}
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 \title{geom_hilight}
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 \usage{
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 geom_hilight(node, fill = "steelblue", alpha = 0.5)
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-
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-stat_hilight(mapping = NULL, data = NULL, geom = "rect",
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-  position = "identity", node, show.legend = NA, inherit.aes = FALSE,
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-  fill, alpha, ...)
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 }
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 \arguments{
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 \item{node}{selected node to hilight}
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@@ -17,16 +12,12 @@ stat_hilight(mapping = NULL, data = NULL, geom = "rect",
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 \item{fill}{color fill}
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 \item{alpha}{alpha (transparency)}
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-
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-\item{geom}{geometric object}
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 }
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 \value{
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 ggplot2
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 }
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 \description{
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 layer of hilight clade with rectangle
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-
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-stat_hilight
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 }
31 22 
 \author{
32 23 
 Guangchuang Yu
Browse code

lots updates

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

g.yu authored on 22/12/2015 04:08:02
Showing 1 changed files
man/geom_hilight.Rd
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@@ -1,23 +1,32 @@
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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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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/geom_hilight.R
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 \name{geom_hilight}
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 \alias{geom_hilight}
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+\alias{stat_hilight}
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 \title{geom_hilight}
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 \usage{
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-geom_hilight(tree_object, node, ...)
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+geom_hilight(node, fill = "steelblue", alpha = 0.5)
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+
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+stat_hilight(mapping = NULL, data = NULL, geom = "rect",
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+  position = "identity", node, show.legend = NA, inherit.aes = FALSE,
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+  fill, alpha, ...)
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 }
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 \arguments{
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-\item{tree_object}{supported tree object}
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+\item{node}{selected node to hilight}
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+
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+\item{fill}{color fill}
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-\item{node}{internal node}
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+\item{alpha}{alpha (transparency)}
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-\item{...}{additional parameters}
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+\item{geom}{geometric object}
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 }
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 \value{
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-ggplot layer
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+ggplot2
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 }
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 \description{
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-hilight clade with rectangle
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+layer of hilight clade with rectangle
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+
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+stat_hilight
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 }
22 31 
 \author{
23 32 
 Guangchuang Yu
Browse code

Commit made by the Bioconductor Git-SVN bridge.

Commit id: ca17acc22b608158936b9c2790bff2f7504f38d9

add author



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

g.yu authored on 27/04/2015 03:15:40
Showing 1 changed files
man/geom_hilight.Rd
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... ... 
@@ -1,4 +1,4 @@
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-% Generated by roxygen2 (4.1.0): do not edit by hand
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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 \name{geom_hilight}
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 \alias{geom_hilight}
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: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@99033 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 04/02/2015 08:24:48
Showing 1 changed files
man/geom_hilight.Rd
History View file @ 1be2c982
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,25 @@
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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_hilight}
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+\alias{geom_hilight}
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+\title{geom_hilight}
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+\usage{
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+geom_hilight(tree_object, node, ...)
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+}
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+\arguments{
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+\item{tree_object}{supported tree object}
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+
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+\item{node}{internal 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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+ggplot layer
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+}
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+\description{
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+hilight clade with rectangle
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+}
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+\author{
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+Guangchuang Yu
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+}
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+