1. ggtree
  2. man
  3. layoutDaylight.Rd
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fix bug of layoutEqualAngle

xiangpin authored on 06/07/2022 13:33:17
Showing 1 changed files
man/layoutDaylight.Rd
History View file @ d2fa81f7
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@@ -21,12 +21,14 @@ tree as data.frame with equal angle layout.
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 }
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 \references{
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 The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm"
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-in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children
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+in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.
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+
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+\if{html}{\out{<div class="sourceCode">}}\preformatted{Leafs are subtrees with no children
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 Initialise tree using equal angle algorithm
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 tree_df = equal_angle(tree)
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 nodes = get list of nodes in tree_df breadth-first
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 nodes = remove tip nodes.
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-}
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+}\if{html}{\out{</div>}}
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 }
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roxygen2md

Guangchuang Yu authored on 01/11/2019 04:24:00
Showing 1 changed files
man/layoutDaylight.Rd
History View file @ 1540db03
... ... 
@@ -21,15 +21,12 @@ tree as data.frame with equal angle layout.
21 21 
 }
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 \references{
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 The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm"
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-in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.
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-
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-```
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-Leafs are subtrees with no children
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+in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children
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 Initialise tree using equal angle algorithm
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 tree_df = equal_angle(tree)
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 nodes = get list of nodes in tree_df breadth-first
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 nodes = remove tip nodes.
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-```
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+}
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 }
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update doc

Guangchuang Yu authored on 02/12/2018 14:13:05
Showing 1 changed files
man/layoutDaylight.Rd
History View file @ 54e7ba29
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@@ -4,12 +4,14 @@
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 \alias{layoutDaylight}
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 \title{Equal daylight layout method for unrooted trees.}
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 \usage{
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-layoutDaylight(model, branch.length)
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+layoutDaylight(model, branch.length, MAX_COUNT = 5)
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 }
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 \arguments{
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 \item{model}{tree object, e.g. phylo or treedata}
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 \item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.}
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+
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+\item{MAX_COUNT}{the maximum number of iterations to run (default 5)}
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 }
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 \value{
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 tree as data.frame with equal angle layout.
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update docs

Guangchuang Yu authored on 11/10/2018 02:44:13
Showing 1 changed files
man/layoutDaylight.Rd
History View file @ b91f9a97
... ... 
@@ -4,10 +4,10 @@
4 4 
 \alias{layoutDaylight}
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 \title{Equal daylight layout method for unrooted trees.}
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 \usage{
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-layoutDaylight(tree, branch.length)
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+layoutDaylight(model, branch.length)
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 }
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 \arguments{
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-\item{tree}{phylo object}
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+\item{model}{tree object, e.g. phylo or treedata}
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 \item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.}
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 }
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clean up code

guangchuang yu authored on 14/12/2017 08:47:21
Showing 1 changed files
man/layoutDaylight.Rd
History View file @ 14ff9149
... ... 
@@ -1,5 +1,5 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/tidytree.R
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+% Please edit documentation in R/tree-utilities.R
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 \name{layoutDaylight}
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 \alias{layoutDaylight}
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 \title{Equal daylight layout method for unrooted trees.}
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geom_motif #148

guangchuang yu authored on 22/08/2017 08:22:37
Showing 1 changed files
man/layoutDaylight.Rd
History View file @ 363c0555
... ... 
@@ -31,4 +31,3 @@ nodes = remove tip nodes.
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 ```
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 }
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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/layoutDaylight.Rd
History View file @ f0e199ad
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@@ -31,3 +31,4 @@ nodes = remove tip nodes.
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 ```
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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/layoutDaylight.Rd
History View file @ 353dfa09
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@@ -31,4 +31,3 @@ nodes = remove tip nodes.
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 ```
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 }
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-
Browse code

day light layout

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@128515 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/04/2017 01:57:57
Showing 1 changed files
man/layoutDaylight.Rd
History View file @ 98e235d8
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new file mode 100644
... ... 
@@ -0,0 +1,34 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/tidytree.R
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+\name{layoutDaylight}
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+\alias{layoutDaylight}
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+\title{Equal daylight layout method for unrooted trees.}
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+\usage{
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+layoutDaylight(tree, branch.length)
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+}
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+\arguments{
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+\item{tree}{phylo object}
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+
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+\item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.}
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+}
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+\value{
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+tree as data.frame with equal angle layout.
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+}
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+\description{
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+#' @title
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+}
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+\references{
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+The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm"
22 
+in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.
23 
+
24 
+```
25 
+Leafs are subtrees with no children
26 
+Initialise tree using equal angle algorithm
27 
+tree_df = equal_angle(tree)
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+
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+nodes = get list of nodes in tree_df breadth-first
30 
+nodes = remove tip nodes.
31 
+
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+```
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+}
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+