git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120045 bc3139a8-67e5-0310-9ffc-ced21a209358
Guangchuang Yu authored on 11/08/2016 06:54:44
| ... | ... |
@@ -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: 1.5.7 |
|
| 4 |
+Version: 1.5.8 |
|
| 5 | 5 |
Author: Guangchuang Yu and Tommy Tsan-Yuk Lam |
| 6 | 6 |
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com> |
| 7 | 7 |
Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. |
| ... | ... |
@@ -1,3 +1,8 @@ |
| 1 |
+CHANGES IN VERSION 1.5.8 |
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| 2 |
+------------------------ |
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| 3 |
+ o add color parameter in geom_cladelabel, color should be of length 1 or 2 <2016-08-11, Thu> |
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| 4 |
+ o geom_cladelabel support parsing expression <2016-08-11, Thu> |
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| 5 |
+ |
|
| 1 | 6 |
CHANGES IN VERSION 1.5.7 |
| 2 | 7 |
------------------------ |
| 3 | 8 |
o geom_strip can accept taxa name as input but labeling strip will not supported. |
| ... | ... |
@@ -12,15 +12,19 @@ |
| 12 | 12 |
##' @param angle angle of text |
| 13 | 13 |
##' @param geom one of 'text' or 'label' |
| 14 | 14 |
##' @param hjust hjust |
| 15 |
+##' @param color color for clade & label, of length 1 or 2 |
|
| 15 | 16 |
##' @param fill fill label background, only work with geom='label' |
| 16 | 17 |
##' @param family sans by default, can be any supported font |
| 18 |
+##' @param parse logical, whether parse label |
|
| 17 | 19 |
##' @param ... additional parameter |
| 18 | 20 |
##' @return ggplot layers |
| 19 | 21 |
##' @export |
| 20 | 22 |
##' @author Guangchuang Yu |
| 21 | 23 |
geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 22 | 24 |
align=FALSE, barsize=0.5, fontsize=3.88, |
| 23 |
- angle=0, geom="text", hjust = 0, fill=NA, family="sans", ...) {
|
|
| 25 |
+ angle=0, geom="text", hjust = 0, |
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+ color = NULL, fill=NA, |
|
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+ family="sans", parse=FALSE, ...) {
|
|
| 24 | 28 |
mapping <- NULL |
| 25 | 29 |
data <- NULL |
| 26 | 30 |
position <- "identity" |
| ... | ... |
@@ -28,30 +32,73 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 28 | 32 |
na.rm <- TRUE |
| 29 | 33 |
inherit.aes <- FALSE |
| 30 | 34 |
|
| 31 |
- if (geom == "text") {
|
|
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- ## no fill parameter |
|
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- layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text, |
|
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- align=align, size=fontsize, angle=angle, family=family, |
|
| 35 |
- mapping=mapping, data=data, geom=geom, hjust=hjust, |
|
| 36 |
- position=position, show.legend = show.legend, |
|
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- inherit.aes = inherit.aes, na.rm=na.rm, ...) |
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- |
|
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+ if (!is.null(color)) {
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+ if (length(color) > 2) {
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+ stop("color should be of length 1 or 2")
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|
| 38 |
+ } |
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+ if (length(color) == 0) {
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| 40 |
+ color = NULL |
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+ } else if (length(color) == 1) {
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|
| 42 |
+ barcolor <- color |
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| 43 |
+ labelcolor <- color |
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+ } else {
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+ barcolor <- color[1] |
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| 46 |
+ labelcolor <- color[2] |
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| 47 |
+ } |
|
| 48 |
+ } |
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| 49 |
+ |
|
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+ if (is.null(color)) {
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|
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+ if (geom == "text") {
|
|
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+ ## no fill parameter |
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+ layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text, |
|
| 54 |
+ align=align, size=fontsize, angle=angle, family=family, |
|
| 55 |
+ mapping=mapping, data=data, geom=geom, hjust=hjust, |
|
| 56 |
+ position=position, show.legend = show.legend, |
|
| 57 |
+ inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...) |
|
| 58 |
+ |
|
| 59 |
+ } else {
|
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+ layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text, |
|
| 61 |
+ align=align, size=fontsize, angle=angle, fill=fill,family=family, |
|
| 62 |
+ mapping=mapping, data=data, geom=geom, hjust=hjust, |
|
| 63 |
+ position=position, show.legend = show.legend, |
|
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+ inherit.aes = inherit.aes, na.rm=na.rm, |
|
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+ parse = parse, ...) |
|
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+ } |
|
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+ |
|
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+ layer_bar <- stat_cladeBar(node=node, offset=offset, align=align, |
|
| 69 |
+ size=barsize, |
|
| 70 |
+ mapping=mapping, data=data, |
|
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+ position=position, show.legend = show.legend, |
|
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+ inherit.aes = inherit.aes, na.rm=na.rm, ...) |
|
| 39 | 73 |
} else {
|
| 40 |
- layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text, |
|
| 41 |
- align=align, size=fontsize, angle=angle, fill=fill,family=family, |
|
| 42 |
- mapping=mapping, data=data, geom=geom, hjust=hjust, |
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- position=position, show.legend = show.legend, |
|
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- inherit.aes = inherit.aes, na.rm=na.rm, ...) |
|
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+ if (geom == "text") {
|
|
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+ ## no fill parameter |
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+ layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text, |
|
| 77 |
+ align=align, size=fontsize, angle=angle, color=labelcolor, family=family, |
|
| 78 |
+ mapping=mapping, data=data, geom=geom, hjust=hjust, |
|
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+ position=position, show.legend = show.legend, |
|
| 80 |
+ inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...) |
|
| 81 |
+ |
|
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+ } else {
|
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+ layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text, |
|
| 84 |
+ align=align, size=fontsize, angle=angle, color=labelcolor, fill=fill,family=family, |
|
| 85 |
+ mapping=mapping, data=data, geom=geom, hjust=hjust, |
|
| 86 |
+ position=position, show.legend = show.legend, |
|
| 87 |
+ inherit.aes = inherit.aes, na.rm=na.rm, |
|
| 88 |
+ parse = parse, ...) |
|
| 89 |
+ } |
|
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+ |
|
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+ layer_bar <- stat_cladeBar(node=node, offset=offset, align=align, |
|
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+ size=barsize, color = barcolor, |
|
| 93 |
+ mapping=mapping, data=data, |
|
| 94 |
+ position=position, show.legend = show.legend, |
|
| 95 |
+ inherit.aes = inherit.aes, na.rm=na.rm, ...) |
|
| 96 |
+ |
|
| 45 | 97 |
} |
| 46 | 98 |
|
| 47 | 99 |
list( |
| 48 |
- stat_cladeBar(node=node, offset=offset, align=align, |
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| 49 |
- size=barsize, |
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| 50 |
- mapping=mapping, data=data, |
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- position=position, show.legend = show.legend, |
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| 52 |
- inherit.aes = inherit.aes, na.rm=na.rm, ...), |
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| 53 |
- |
|
| 54 |
- layer_text |
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| 100 |
+ layer_bar, |
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| 101 |
+ layer_text |
|
| 55 | 102 |
) |
| 56 | 103 |
} |
| 57 | 104 |
|
| ... | ... |
@@ -59,7 +106,8 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 59 | 106 |
stat_cladeText <- function(mapping=NULL, data=NULL, |
| 60 | 107 |
geom="text", position="identity", |
| 61 | 108 |
node, label, offset, align, ..., |
| 62 |
- show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
|
|
| 109 |
+ show.legend=NA, inherit.aes=FALSE, |
|
| 110 |
+ na.rm=FALSE, parse=FALSE) {
|
|
| 63 | 111 |
default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent) |
| 64 | 112 |
if (is.null(mapping)) {
|
| 65 | 113 |
mapping <- default_aes |
| ... | ... |
@@ -75,10 +123,11 @@ stat_cladeText <- function(mapping=NULL, data=NULL, |
| 75 | 123 |
show.legend = show.legend, |
| 76 | 124 |
inherit.aes = inherit.aes, |
| 77 | 125 |
params=list(node=node, |
| 78 |
- label=label, |
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| 79 |
- offset=offset, |
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| 80 |
- align=align, |
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| 81 |
- na.rm=na.rm, |
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+ label = label, |
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+ offset = offset, |
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| 128 |
+ align = align, |
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+ na.rm = na.rm, |
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+ parse = parse, |
|
| 82 | 131 |
...) |
| 83 | 132 |
) |
| 84 | 133 |
|
| ... | ... |
@@ -88,7 +137,7 @@ stat_cladeBar <- function(mapping=NULL, data=NULL, |
| 88 | 137 |
geom="segment", position="identity", |
| 89 | 138 |
node, offset, align, ..., |
| 90 | 139 |
show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
|
| 91 |
- default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent) |
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| 140 |
+ default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, xend=~x, yend=~y) |
|
| 92 | 141 |
if (is.null(mapping)) {
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| 93 | 142 |
mapping <- default_aes |
| 94 | 143 |
} else {
|
| ... | ... |
@@ -14,7 +14,7 @@ geom_range <- function(range="height_0.95_HPD", ...) {
|
| 14 | 14 |
na.rm = TRUE |
| 15 | 15 |
inherit.aes = FALSE |
| 16 | 16 |
|
| 17 |
- default_aes <- aes_(x=~x, y=~y) |
|
| 17 |
+ default_aes <- aes_(x=~x, y=~y, xend=~x, yend=~y) |
|
| 18 | 18 |
|
| 19 | 19 |
mapping <- modifyList(default_aes, aes_string(branch.length="branch.length", label=range)) |
| 20 | 20 |
|
| ... | ... |
@@ -105,7 +105,7 @@ stat_stripBar <- function(mapping=NULL, data=NULL, |
| 105 | 105 |
show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
|
| 106 | 106 |
|
| 107 | 107 |
if (is.null(label) || is.na(label)) {
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| 108 |
- default_aes <- aes_(x=~x, y=~y, node=~node, label=~label) |
|
| 108 |
+ default_aes <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y) |
|
| 109 | 109 |
} else {
|
| 110 | 110 |
default_aes <- aes_(x=~x, y=~y, node=~node) |
| 111 | 111 |
} |
| ... | ... |
@@ -18,10 +18,10 @@ geom_taxalink <- function(taxa1, taxa2, curvature=0.5, ...) {
|
| 18 | 18 |
na.rm = TRUE |
| 19 | 19 |
inherit.aes = FALSE |
| 20 | 20 |
|
| 21 |
- mapping <- aes_(x=~x, y=~y, node=~node, label=~label) |
|
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+ mapping <- aes_(x=~x, y=~y, node=~node, label=~label, xend=~x, yend=~y) |
|
| 22 | 22 |
|
| 23 | 23 |
layer(stat=StatTaxalink, |
| 24 |
- mapping=aes_(x=~x, y=~y, node=~node, label=~label), |
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+ mapping=mapping, |
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| 25 | 25 |
geom=GeomCurve, |
| 26 | 26 |
position='identity', |
| 27 | 27 |
show.legend=show.legend, |
| ... | ... |
@@ -45,7 +45,7 @@ stat_treeScaleLine <- function(mapping=NULL, data=NULL, |
| 45 | 45 |
xx, yy, width, offset, color, ..., |
| 46 | 46 |
show.legend=NA, inherit.aes=FALSE, na.rm=FALSE){
|
| 47 | 47 |
|
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- default_aes <- aes_(x=~x, y=~y) |
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+ default_aes <- aes_(x=~x, y=~y, xend=~x, yend=~y) |
|
| 49 | 49 |
if (is.null(mapping)) {
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| 50 | 50 |
mapping <- default_aes |
| 51 | 51 |
} else {
|
| ... | ... |
@@ -74,7 +74,7 @@ stat_treeScaleText <- function(mapping=NULL, data=NULL, |
| 74 | 74 |
xx, yy, width, offset, color, ..., |
| 75 | 75 |
show.legend=NA, inherit.aes=TRUE, na.rm=FALSE) {
|
| 76 | 76 |
|
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- default_aes <- aes_(x=~x, y=~y) |
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+ default_aes <- aes_(x=~x, y=~y, label=~label) |
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| 78 | 78 |
if (is.null(mapping)) {
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| 79 | 79 |
mapping <- default_aes |
| 80 | 80 |
} else {
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| 81 | 81 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,59 @@ |
| 1 |
+ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
|
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+=========================================================================================================================== |
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+ |
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+[](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) |
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+ |
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+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) |
|
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+ |
|
| 8 |
+[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://support.bioconductor.org/t/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree/) |
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+ |
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+The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. |
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+ |
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+------------------------------------------------------------------------ |
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+ |
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+Please cite the following article when using `ggtree`: |
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+ |
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+**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***. *accepted* |
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+ |
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+[](https://twitter.com/intent/tweet?hashtags=ggtree&url=https://guangchuangyu.github.io/ggtree) |
|
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+ |
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+------------------------------------------------------------------------ |
|
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+ |
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+For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>. |
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+ |
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+- [Documentation](https://guangchuangyu.github.io/ggtree/documentation/) |
|
| 25 |
+- [FAQ](https://guangchuangyu.github.io/ggtree/faq/) |
|
| 26 |
+- [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/) |
|
| 27 |
+- [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) |
|
| 28 |
+ |
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+### Example |
|
| 30 |
+ |
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+[](https://guangchuangyu.github.io/ggtree/featuredArticles/) |
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+ |
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+### Download stats |
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+ |
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+ +---------------------------+---------------------------+----------------------------+--------+ |
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+ | * | |
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+ 1200 + + |
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+ | * | |
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+ | * | |
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+ 1000 + * * + |
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+ | | |
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+ | | |
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+ | | |
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+ 800 + * * + |
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+ | * | |
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+ | * * | |
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+ 600 + * + |
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+ | | |
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+ | | |
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+ | * | |
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+ 400 + * * + |
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+ | * | |
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+ | | |
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+ 200 + * + |
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+ | | |
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+ | | |
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+ | * * * | |
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+ 0 +---------------------------+---------------------------+----------------------------+--------+ |
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+ 2015.5 2016 2016.5 |
| ... | ... |
@@ -6,7 +6,7 @@ |
| 6 | 6 |
\usage{
|
| 7 | 7 |
geom_cladelabel(node, label, offset = 0, offset.text = 0, align = FALSE, |
| 8 | 8 |
barsize = 0.5, fontsize = 3.88, angle = 0, geom = "text", hjust = 0, |
| 9 |
- fill = NA, family = "sans", ...) |
|
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+ color = NULL, fill = NA, family = "sans", parse = FALSE, ...) |
|
| 10 | 10 |
} |
| 11 | 11 |
\arguments{
|
| 12 | 12 |
\item{node}{selected node}
|
| ... | ... |
@@ -29,10 +29,14 @@ geom_cladelabel(node, label, offset = 0, offset.text = 0, align = FALSE, |
| 29 | 29 |
|
| 30 | 30 |
\item{hjust}{hjust}
|
| 31 | 31 |
|
| 32 |
+\item{color}{color for clade & label, of length 1 or 2}
|
|
| 33 |
+ |
|
| 32 | 34 |
\item{fill}{fill label background, only work with geom='label'}
|
| 33 | 35 |
|
| 34 | 36 |
\item{family}{sans by default, can be any supported font}
|
| 35 | 37 |
|
| 38 |
+\item{parse}{logical, whether parse label}
|
|
| 39 |
+ |
|
| 36 | 40 |
\item{...}{additional parameter}
|
| 37 | 41 |
} |
| 38 | 42 |
\value{
|
| 39 | 43 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,9 @@ |
| 1 |
+context('geom_cladelabel')
|
|
| 2 |
+ |
|
| 3 |
+ |
|
| 4 |
+test_that('geom_cladelabel support parsing expression', {
|
|
| 5 |
+ p <- ggtree(rtree(30)) + geom_cladelabel(node=40, label='paste(italic("species name"), "accession number")', parse=T)
|
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+ expect_true(is.ggplot(p)) |
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+}) |
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+ |
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+ |