| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: ggtree |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: an R package for visualization of tree and annotation data |
| 4 |
-Version: 3.4.1 |
|
| 4 |
+Version: 3.4.2 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"),
|
| 7 | 7 |
comment = c(ORCID = "0000-0002-6485-8781")), |
| ... | ... |
@@ -57,10 +57,10 @@ VignetteBuilder: knitr |
| 57 | 57 |
ByteCompile: true |
| 58 | 58 |
Encoding: UTF-8 |
| 59 | 59 |
License: Artistic-2.0 |
| 60 |
-URL: https://yulab-smu.top/treedata-book/ (book), http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628 (paper) |
|
| 60 |
+URL: https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/ (book), http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628 (paper) |
|
| 61 | 61 |
BugReports: https://github.com/YuLab-SMU/ggtree/issues |
| 62 | 62 |
Packaged: 2014-12-03 08:16:14 UTC; root |
| 63 | 63 |
biocViews: Alignment, Annotation, Clustering, DataImport, |
| 64 | 64 |
MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization |
| 65 |
-RoxygenNote: 7.1.2 |
|
| 65 |
+RoxygenNote: 7.2.1 |
|
| 66 | 66 |
Roxygen: list(markdown = TRUE) |
| ... | ... |
@@ -1,5 +1,17 @@ |
| 1 | 1 |
citHeader("To cite ggtree in publications use:")
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| 2 | 2 |
|
| 3 |
+citEntry( |
|
| 4 |
+ entry = "book", |
|
| 5 |
+ title = "Data Integration, Manipulation and Visualization of Phylogenetic Treess", |
|
| 6 |
+ author = person("Guangchuang", "Yu"),
|
|
| 7 |
+ publisher = "Chapman and Hall/{CRC}",
|
|
| 8 |
+ year = "2022", |
|
| 9 |
+ edition = "1st edition", |
|
| 10 |
+ textVersion = paste("Guangchuang Yu. (2022).",
|
|
| 11 |
+ "Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).", |
|
| 12 |
+ "Chapman and Hall/CRC.") |
|
| 13 |
+) |
|
| 14 |
+ |
|
| 3 | 15 |
citEntry( |
| 4 | 16 |
entry = "article", |
| 5 | 17 |
title = "Using ggtree to Visualize Data on Tree-Like Structures", |
| ... | ... |
@@ -21,12 +21,14 @@ tree as data.frame with equal angle layout. |
| 21 | 21 |
} |
| 22 | 22 |
\references{
|
| 23 | 23 |
The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm" |
| 24 |
-in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.\preformatted{Leafs are subtrees with no children
|
|
| 24 |
+in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein. |
|
| 25 |
+ |
|
| 26 |
+\if{html}{\out{<div class="sourceCode">}}\preformatted{Leafs are subtrees with no children
|
|
| 25 | 27 |
Initialise tree using equal angle algorithm |
| 26 | 28 |
tree_df = equal_angle(tree) |
| 27 | 29 |
|
| 28 | 30 |
nodes = get list of nodes in tree_df breadth-first |
| 29 | 31 |
nodes = remove tip nodes. |
| 30 | 32 |
|
| 31 |
-} |
|
| 33 |
+}\if{html}{\out{</div>}}
|
|
| 32 | 34 |
} |
| ... | ... |
@@ -52,6 +52,6 @@ below to see their documentation. |
| 52 | 52 |
|
| 53 | 53 |
\item{magrittr}{\code{\link[magrittr:pipe]{\%>\%}}}
|
| 54 | 54 |
|
| 55 |
- \item{tidytree}{\code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 55 |
+ \item{tidytree}{\code{\link[tidytree]{groupClade}}, \code{\link[tidytree]{groupOTU}}, \code{\link[tidytree]{MRCA}}, \code{\link[tidytree]{nodeid}}, \code{\link[tidytree]{nodelab}}}
|
|
| 56 | 56 |
}} |
| 57 | 57 |
|
