| ... | ... |
@@ -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: 1.7.9 |
|
| 4 |
+Version: 1.7.10 |
|
| 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 +1,7 @@ |
| 1 |
+CHANGES IN VERSION 1.7.10 |
|
| 2 |
+------------------------ |
|
| 3 |
+ o update subview to support mainview produced by `ggplot() + layers` <2017-03-13, Mon> |
|
| 4 |
+ |
|
| 1 | 5 |
CHANGES IN VERSION 1.7.9 |
| 2 | 6 |
------------------------ |
| 3 | 7 |
o fixed geom_range to support height_0.95_HPD <2017-03-03, Fri> |
| ... | ... |
@@ -1,6 +1,6 @@ |
| 1 | 1 |
##' add subview to mainview for ggplot2 objects |
| 2 | 2 |
##' |
| 3 |
-##' |
|
| 3 |
+##' |
|
| 4 | 4 |
##' @title subview |
| 5 | 5 |
##' @param mainview main view |
| 6 | 6 |
##' @param subview a ggplot or grob object |
| ... | ... |
@@ -11,15 +11,22 @@ |
| 11 | 11 |
##' @return ggplot object |
| 12 | 12 |
##' @importFrom ggplot2 annotation_custom |
| 13 | 13 |
##' @importFrom ggplot2 ggplotGrob |
| 14 |
+##' @importFrom ggplot2 ggplot_build |
|
| 14 | 15 |
##' @export |
| 15 | 16 |
##' @author Guangchuang Yu |
| 16 | 17 |
subview <- function(mainview, subview, x, y, width=.1, height=.1) {
|
| 17 | 18 |
mapping <- mainview$mapping %>% as.character |
| 18 | 19 |
aes_x <- mapping["x"] |
| 19 | 20 |
aes_y <- mapping["y"] |
| 20 |
- |
|
| 21 |
- xrng <- mainview$data[, aes_x] %>% range |
|
| 22 |
- yrng <- mainview$data[, aes_y] %>% range |
|
| 21 |
+ |
|
| 22 |
+ if (is.na(aes_x) || is.na(aes_y)) {
|
|
| 23 |
+ obj <- ggplot_build(mainview) |
|
| 24 |
+ xrng <- obj$layout$panel_ranges[[1]]$x.range |
|
| 25 |
+ yrng <- obj$layout$panel_ranges[[1]]$y.range |
|
| 26 |
+ } else {
|
|
| 27 |
+ xrng <- mainview$data[, aes_x] %>% range |
|
| 28 |
+ yrng <- mainview$data[, aes_y] %>% range |
|
| 29 |
+ } |
|
| 23 | 30 |
|
| 24 | 31 |
for (i in seq_along(mainview$layers)) {
|
| 25 | 32 |
layer <- mainview$layers[[i]] |
| ... | ... |
@@ -58,11 +65,11 @@ subview <- function(mainview, subview, x, y, width=.1, height=.1) {
|
| 58 | 65 |
|
| 59 | 66 |
xrng <- diff(xrng) |
| 60 | 67 |
yrng <- diff(yrng) |
| 61 |
- |
|
| 68 |
+ |
|
| 62 | 69 |
if (!any(class(subview) %in% c("ggplot", "grob", "character"))) {
|
| 63 | 70 |
stop("subview should be a ggplot or grob object, or an image file...")
|
| 64 | 71 |
} |
| 65 |
- |
|
| 72 |
+ |
|
| 66 | 73 |
if (is(subview, "ggplot")) {
|
| 67 | 74 |
sv <- ggplotGrob(subview) |
| 68 | 75 |
} else if (is(subview, "grob")) {
|
| ... | ... |
@@ -76,7 +83,7 @@ subview <- function(mainview, subview, x, y, width=.1, height=.1) {
|
| 76 | 83 |
|
| 77 | 84 |
width <- width/2 |
| 78 | 85 |
height <- height/2 |
| 79 |
- |
|
| 86 |
+ |
|
| 80 | 87 |
mainview + annotation_custom( |
| 81 | 88 |
sv, |
| 82 | 89 |
xmin = x - width*xrng, |
| ... | ... |
@@ -19,7 +19,7 @@ library("ypages")
|
| 19 | 19 |
|
| 20 | 20 |
|
| 21 | 21 |
`r badge_bioc_release("ggtree", "green")`
|
| 22 |
-`r badge_devel("ggtree", "green")`
|
|
| 22 |
+`r badge_devel("guangchuangyu/ggtree", "green")`
|
|
| 23 | 23 |
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) |
| 24 | 24 |
`r badge_bioc_download("ggtree", "total", "blue")`
|
| 25 | 25 |
`r badge_bioc_download("ggtree", "month", "blue")`
|
| ... | ... |
@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with |
| 4 | 4 |
|
| 5 | 5 |
<img src="https://raw.githubusercontent.com/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" /> |
| 6 | 6 |
|
| 7 |
-[](https://bioconductor.org/packages/ggtree) [](https://github.com/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) |
|
| 7 |
+[](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) |
|
| 8 | 8 |
|
| 9 |
-[](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) |
|
| 9 |
+[](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) |
|
| 10 | 10 |
|
| 11 | 11 |
[](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) |
| 12 | 12 |
|
| ... | ... |
@@ -20,7 +20,7 @@ Please cite the following article when using `ggtree`: |
| 20 | 20 |
|
| 21 | 21 |
**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36. |
| 22 | 22 |
|
| 23 |
-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [](https://www.altmetric.com/details/10533079) |
|
| 23 |
+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [](https://www.altmetric.com/details/10533079) |
|
| 24 | 24 |
|
| 25 | 25 |
------------------------------------------------------------------------ |
| 26 | 26 |
|
| ... | ... |
@@ -33,32 +33,32 @@ For details, please visit our project website, <https://guangchuangyu.github.io/ |
| 33 | 33 |
|
| 34 | 34 |
### Citation |
| 35 | 35 |
|
| 36 |
-[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 36 |
+[](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 37 | 37 |
|
| 38 | 38 |
+--+---------+---------+---------+---------+---------+---+ |
| 39 |
- 7 + * + |
|
| 39 |
+ 8 + * + |
|
| 40 |
+ | | |
|
| 40 | 41 |
| | |
| 41 | 42 |
6 + + |
| 42 | 43 |
| | |
| 43 |
- 5 + + |
|
| 44 | 44 |
| | |
| 45 | 45 |
4 + + |
| 46 |
- 3 + + |
|
| 47 | 46 |
| | |
| 48 |
- 2 + + |
|
| 49 | 47 |
| | |
| 50 |
- 1 + * + |
|
| 48 |
+ | | |
|
| 49 |
+ 2 + + |
|
| 50 |
+ | * | |
|
| 51 | 51 |
+--+---------+---------+---------+---------+---------+---+ |
| 52 | 52 |
2016 2016.2 2016.4 2016.6 2016.8 2017 |
| 53 | 53 |
|
| 54 | 54 |
### Download stats |
| 55 | 55 |
|
| 56 |
-[](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 56 |
+[](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
| 57 | 57 |
|
| 58 | 58 |
++-------------------+-------------------+--------------------+-------------------+-----------+ |
| 59 | 59 |
| * | |
| 60 |
- | * | |
|
| 61 |
- | * | |
|
| 60 |
+ | * * | |
|
| 61 |
+ | | |
|
| 62 | 62 |
| * * | |
| 63 | 63 |
| | |
| 64 | 64 |
1500 + + |
