| ... | ... |
@@ -1,3 +1,7 @@ |
| 1 |
+# Bradley Jones |
|
| 2 |
+ |
|
| 3 |
++ made data usable with treedata in 'equal_angle' and 'daylight' layouts |
|
| 4 |
+ - <https://github.com/GuangchuangYu/ggtree/pull/201> |
|
| 1 | 5 |
|
| 2 | 6 |
# Justin Silverman |
| 3 | 7 |
|
| ... | ... |
@@ -17,3 +21,4 @@ |
| 17 | 21 |
+ Refactor layoutDaylight |
| 18 | 22 |
- <https://github.com/GuangchuangYu/ggtree/pull/165> |
| 19 | 23 |
- <https://github.com/GuangchuangYu/ggtree/pull/169> |
| 24 |
+ |
| ... | ... |
@@ -2,11 +2,12 @@ Package: ggtree |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: an R package for visualization and annotation of phylogenetic trees with |
| 4 | 4 |
their covariates and other associated data |
| 5 |
-Version: 1.13.5 |
|
| 5 |
+Version: 1.13.6 |
|
| 6 | 6 |
Authors@R: c( |
| 7 | 7 |
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
|
| 8 | 8 |
person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", role = c("aut", "ths")),
|
| 9 | 9 |
person("Justin", "Silverman", email = "jsilve24@gmail.com", role = "ctb"),
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| 10 |
+ person("Bradley", "Jones", email = "brj1@sfu.ca", role = "ctb"),
|
|
| 10 | 11 |
person("Watal M.", "Iwasaki", email = "heavy.watal@gmail.com", role = "ctb")
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| 11 | 12 |
) |
| 12 | 13 |
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com> |
| ... | ... |
@@ -1,3 +1,8 @@ |
| 1 |
+# ggtree 1.13.6 |
|
| 2 |
+ |
|
| 3 |
++ made data usable with treedata in 'equal_angle' and 'daylight' layouts (2018-10-11, Thu) |
|
| 4 |
+ - <https://github.com/GuangchuangYu/ggtree/pull/201> |
|
| 5 |
+ |
|
| 1 | 6 |
# ggtree 1.13.5 |
| 2 | 7 |
|
| 3 | 8 |
+ enable additional parameters passed to `geom_rootedge` (2018-09-13, Thu) |
| ... | ... |
@@ -7,7 +7,7 @@ layout.unrooted <- function(model, branch.length="branch.length", layout.method= |
| 7 | 7 |
equal_angle = layoutEqualAngle(model, branch.length), |
| 8 | 8 |
daylight = layoutDaylight(model, branch.length) |
| 9 | 9 |
) |
| 10 |
- |
|
| 10 |
+ |
|
| 11 | 11 |
return(df) |
| 12 | 12 |
} |
| 13 | 13 |
|
| ... | ... |
@@ -33,21 +33,28 @@ set_branch_length_cladogram <- function(tree) {
|
| 33 | 33 |
##' "Inferring Phylogenies" by Joseph Felsenstein. |
| 34 | 34 |
##' |
| 35 | 35 |
##' @title layoutEqualAngle |
| 36 |
-##' @param tree phylo object |
|
| 36 |
+##' @param model tree object, e.g. phylo or treedata |
|
| 37 | 37 |
##' @param branch.length set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used. |
| 38 | 38 |
##' @return tree as data.frame with equal angle layout. |
| 39 | 39 |
layoutEqualAngle <- function(model, branch.length ){
|
| 40 | 40 |
tree <- as.phylo(model) |
| 41 |
- |
|
| 42 |
- if (branch.length == "none") {
|
|
| 43 |
- tree <- set_branch_length_cladogram(tree) |
|
| 44 |
- } |
|
| 45 | 41 |
|
| 46 |
- root <- getRoot(tree) |
|
| 47 |
- ## Convert Phylo tree to data.frame. |
|
| 48 |
- ## df <- as.data.frame.phylo_(tree) |
|
| 49 |
- df <- as_data_frame(model) %>% |
|
| 50 |
- mutate_(isTip = ~(! node %in% parent)) |
|
| 42 |
+ if (! is.null(tree$edge.length)) {
|
|
| 43 |
+ if (anyNA(tree$edge.length)) {
|
|
| 44 |
+ warning("'edge.length' contains NA values...\n## setting 'edge.length' to NULL automatically when plotting the tree...")
|
|
| 45 |
+ tree$edge.length <- NULL |
|
| 46 |
+ } |
|
| 47 |
+ } |
|
| 48 |
+ |
|
| 49 |
+ if (branch.length == "none") {
|
|
| 50 |
+ tree <- set_branch_length_cladogram(tree) |
|
| 51 |
+ } |
|
| 52 |
+ |
|
| 53 |
+ root <- getRoot(tree) |
|
| 54 |
+ ## Convert Phylo tree to data.frame. |
|
| 55 |
+ ## df <- as.data.frame.phylo_(tree) |
|
| 56 |
+ df <- as_data_frame(model) %>% |
|
| 57 |
+ mutate_(isTip = ~(! node %in% parent)) |
|
| 51 | 58 |
|
| 52 | 59 |
## NOTE: Angles (start, end, angle) are in half-rotation units (radians/pi or degrees/180) |
| 53 | 60 |
|
| ... | ... |
@@ -113,7 +120,7 @@ layoutEqualAngle <- function(model, branch.length ){
|
| 113 | 120 |
##' Equal daylight layout method for unrooted trees. |
| 114 | 121 |
##' |
| 115 | 122 |
##' #' @title |
| 116 |
-##' @param tree phylo object |
|
| 123 |
+##' @param model tree object, e.g. phylo or treedata |
|
| 117 | 124 |
##' @param branch.length set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used. |
| 118 | 125 |
##' @return tree as data.frame with equal angle layout. |
| 119 | 126 |
##' @references |
| ... | ... |
@@ -4,10 +4,10 @@ |
| 4 | 4 |
\alias{layoutDaylight}
|
| 5 | 5 |
\title{Equal daylight layout method for unrooted trees.}
|
| 6 | 6 |
\usage{
|
| 7 |
-layoutDaylight(tree, branch.length) |
|
| 7 |
+layoutDaylight(model, branch.length) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{tree}{phylo object}
|
|
| 10 |
+\item{model}{tree object, e.g. phylo or treedata}
|
|
| 11 | 11 |
|
| 12 | 12 |
\item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.}
|
| 13 | 13 |
} |
| ... | ... |
@@ -4,10 +4,10 @@ |
| 4 | 4 |
\alias{layoutEqualAngle}
|
| 5 | 5 |
\title{layoutEqualAngle}
|
| 6 | 6 |
\usage{
|
| 7 |
-layoutEqualAngle(tree, branch.length) |
|
| 7 |
+layoutEqualAngle(model, branch.length) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 |
-\item{tree}{phylo object}
|
|
| 10 |
+\item{model}{tree object, e.g. phylo or treedata}
|
|
| 11 | 11 |
|
| 12 | 12 |
\item{branch.length}{set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.}
|
| 13 | 13 |
} |
