| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: ggtree |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
| 4 |
-Version: 1.7.8 |
|
| 4 |
+Version: 1.7.9 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
|
| 7 | 7 |
person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
|
| ... | ... |
@@ -1,3 +1,8 @@ |
| 1 |
+CHANGES IN VERSION 1.7.9 |
|
| 2 |
+------------------------ |
|
| 3 |
+ o fixed geom_tiplab(geom='label') <2017-03-02, Thu> |
|
| 4 |
+ + https://github.com/GuangchuangYu/ggtree/issues/115 |
|
| 5 |
+ |
|
| 1 | 6 |
CHANGES IN VERSION 1.7.8 |
| 2 | 7 |
------------------------ |
| 3 | 8 |
o get_taxa_name now sorted by taxa position and also support whole tree <2017-03-01, Wed> |
| ... | ... |
@@ -6,6 +6,7 @@ |
| 6 | 6 |
##' @param data A layer specific dataset - |
| 7 | 7 |
##' only needed if you want to override he plot defaults. |
| 8 | 8 |
##' @param ... other arguments passed on to 'layer' |
| 9 |
+##' @param position The position adjustment to use for overlapping points on this layer |
|
| 9 | 10 |
##' @param family sans by default, can be any supported font |
| 10 | 11 |
##' @param parse if TRUE, the labels will be passd into expressions |
| 11 | 12 |
##' @param nudge_x horizontal adjustment |
| ... | ... |
@@ -25,6 +26,7 @@ |
| 25 | 26 |
##' @author Guangchuang Yu |
| 26 | 27 |
geom_label2 <- function(mapping = NULL, data = NULL, |
| 27 | 28 |
..., |
| 29 |
+ position = "identity", |
|
| 28 | 30 |
family = "sans", |
| 29 | 31 |
parse = FALSE, |
| 30 | 32 |
nudge_x = 0, |
| ... | ... |
@@ -36,8 +38,6 @@ geom_label2 <- function(mapping = NULL, data = NULL, |
| 36 | 38 |
show.legend = NA, |
| 37 | 39 |
inherit.aes = TRUE) {
|
| 38 | 40 |
|
| 39 |
- position = "identity" |
|
| 40 |
- |
|
| 41 | 41 |
if (!missing(nudge_x) || !missing(nudge_y)) {
|
| 42 | 42 |
if (!missing(position)) {
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| 43 | 43 |
stop("Specify either `position` or `nudge_x`/`nudge_y`", call. = FALSE)
|
| ... | ... |
@@ -5,13 +5,13 @@ |
| 5 | 5 |
##' @param mapping the aesthetic mapping |
| 6 | 6 |
##' @param data A layer specific dataset - |
| 7 | 7 |
##' only needed if you want to override he plot defaults. |
| 8 |
+##' @param ... other arguments passed on to 'layer' |
|
| 8 | 9 |
##' @param position The position adjustment to use for overlapping points on this layer |
| 9 | 10 |
##' @param family sans by default, can be any supported font |
| 10 | 11 |
##' @param parse if TRUE, the labels will be passd into expressions |
| 11 | 12 |
##' @param na.rm logical |
| 12 | 13 |
##' @param show.legend logical |
| 13 | 14 |
##' @param inherit.aes logical |
| 14 |
-##' @param ... other arguments passed on to 'layer' |
|
| 15 | 15 |
##' @param nudge_x horizontal adjustment |
| 16 | 16 |
##' @param nudge_y vertical adjustment |
| 17 | 17 |
##' @param check_overlap if TRUE, text that overlaps previous text in the same layer will not be plotted |
| ... | ... |
@@ -24,9 +24,16 @@ |
| 24 | 24 |
##' \link[ggplot2]{geom_text}
|
| 25 | 25 |
##' @author Guangchuang Yu |
| 26 | 26 |
geom_text2 <- function(mapping = NULL, data = NULL, |
| 27 |
- position = "identity", family="sans", parse = FALSE, |
|
| 28 |
- na.rm=TRUE, show.legend = NA, inherit.aes = TRUE, |
|
| 29 |
- ..., nudge_x = 0, nudge_y = 0, check_overlap = FALSE) {
|
|
| 27 |
+ ..., |
|
| 28 |
+ position = "identity", |
|
| 29 |
+ family="sans", |
|
| 30 |
+ parse = FALSE, |
|
| 31 |
+ na.rm=TRUE, |
|
| 32 |
+ show.legend = NA, |
|
| 33 |
+ inherit.aes = TRUE, |
|
| 34 |
+ nudge_x = 0, |
|
| 35 |
+ nudge_y = 0, |
|
| 36 |
+ check_overlap = FALSE) {
|
|
| 30 | 37 |
|
| 31 | 38 |
if (!missing(nudge_x) || !missing(nudge_y)) {
|
| 32 | 39 |
if (!missing(position)) {
|
| ... | ... |
@@ -2,9 +2,9 @@ |
| 2 | 2 |
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
| 3 | 3 |
=========================================================================================================================== |
| 4 | 4 |
|
| 5 |
-[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" /> |
|
| 5 |
+[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" /> |
|
| 6 | 6 |
|
| 7 |
-[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
| 7 |
+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
| 8 | 8 |
|
| 9 | 9 |
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [](https://travis-ci.org/GuangchuangYu/ggtree) [](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html) |
| 10 | 10 |
|
| ... | ... |
@@ -4,10 +4,10 @@ |
| 4 | 4 |
\alias{geom_label2}
|
| 5 | 5 |
\title{geom_label2}
|
| 6 | 6 |
\usage{
|
| 7 |
-geom_label2(mapping = NULL, data = NULL, ..., family = "sans", |
|
| 8 |
- parse = FALSE, nudge_x = 0, nudge_y = 0, label.padding = unit(0.25, |
|
| 9 |
- "lines"), label.r = unit(0.15, "lines"), label.size = 0.25, |
|
| 10 |
- na.rm = TRUE, show.legend = NA, inherit.aes = TRUE) |
|
| 7 |
+geom_label2(mapping = NULL, data = NULL, ..., position = "identity", |
|
| 8 |
+ family = "sans", parse = FALSE, nudge_x = 0, nudge_y = 0, |
|
| 9 |
+ label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"), |
|
| 10 |
+ label.size = 0.25, na.rm = TRUE, show.legend = NA, inherit.aes = TRUE) |
|
| 11 | 11 |
} |
| 12 | 12 |
\arguments{
|
| 13 | 13 |
\item{mapping}{the aesthetic mapping}
|
| ... | ... |
@@ -17,6 +17,8 @@ only needed if you want to override he plot defaults.} |
| 17 | 17 |
|
| 18 | 18 |
\item{...}{other arguments passed on to 'layer'}
|
| 19 | 19 |
|
| 20 |
+\item{position}{The position adjustment to use for overlapping points on this layer}
|
|
| 21 |
+ |
|
| 20 | 22 |
\item{family}{sans by default, can be any supported font}
|
| 21 | 23 |
|
| 22 | 24 |
\item{parse}{if TRUE, the labels will be passd into expressions}
|
| ... | ... |
@@ -4,10 +4,9 @@ |
| 4 | 4 |
\alias{geom_text2}
|
| 5 | 5 |
\title{geom_text2}
|
| 6 | 6 |
\usage{
|
| 7 |
-geom_text2(mapping = NULL, data = NULL, position = "identity", |
|
| 7 |
+geom_text2(mapping = NULL, data = NULL, ..., position = "identity", |
|
| 8 | 8 |
family = "sans", parse = FALSE, na.rm = TRUE, show.legend = NA, |
| 9 |
- inherit.aes = TRUE, ..., nudge_x = 0, nudge_y = 0, |
|
| 10 |
- check_overlap = FALSE) |
|
| 9 |
+ inherit.aes = TRUE, nudge_x = 0, nudge_y = 0, check_overlap = FALSE) |
|
| 11 | 10 |
} |
| 12 | 11 |
\arguments{
|
| 13 | 12 |
\item{mapping}{the aesthetic mapping}
|
| ... | ... |
@@ -15,6 +14,8 @@ geom_text2(mapping = NULL, data = NULL, position = "identity", |
| 15 | 14 |
\item{data}{A layer specific dataset -
|
| 16 | 15 |
only needed if you want to override he plot defaults.} |
| 17 | 16 |
|
| 17 |
+\item{...}{other arguments passed on to 'layer'}
|
|
| 18 |
+ |
|
| 18 | 19 |
\item{position}{The position adjustment to use for overlapping points on this layer}
|
| 19 | 20 |
|
| 20 | 21 |
\item{family}{sans by default, can be any supported font}
|
| ... | ... |
@@ -27,8 +28,6 @@ only needed if you want to override he plot defaults.} |
| 27 | 28 |
|
| 28 | 29 |
\item{inherit.aes}{logical}
|
| 29 | 30 |
|
| 30 |
-\item{...}{other arguments passed on to 'layer'}
|
|
| 31 |
- |
|
| 32 | 31 |
\item{nudge_x}{horizontal adjustment}
|
| 33 | 32 |
|
| 34 | 33 |
\item{nudge_y}{vertical adjustment}
|
