guangchuang yu authored on 26/07/2017 02:13:53
| ... | ... |
@@ -43,4 +43,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues |
| 43 | 43 |
Packaged: 2014-12-03 08:16:14 UTC; root |
| 44 | 44 |
biocViews: Alignment, Annotation, Clustering, DataImport, |
| 45 | 45 |
MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization |
| 46 |
-RoxygenNote: 5.0.1 |
|
| 46 |
+RoxygenNote: 6.0.1 |
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.9.2 |
| 2 | 2 |
------------------------ |
| 3 |
+ o extend parameter in geom_cladebar <2017-07-26, Wed> |
|
| 4 |
+ + https://github.com/GuangchuangYu/ggtree/issues/142#issuecomment-317817995 |
|
| 3 | 5 |
o scaleClade works after calling viewClade <2017-07-20, Thu> |
| 4 | 6 |
+ https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!topic/bioc-ggtree/QVSryszPaFY |
| 5 | 7 |
o gheatmap support handling collapsed tree <2017-06-29, Thu> |
| ... | ... |
@@ -6,6 +6,7 @@ |
| 6 | 6 |
##' @param label clade label |
| 7 | 7 |
##' @param offset offset of bar and text from the clade |
| 8 | 8 |
##' @param offset.text offset of text from bar |
| 9 |
+##' @param extend extend bar height |
|
| 9 | 10 |
##' @param align logical |
| 10 | 11 |
##' @param barsize size of bar |
| 11 | 12 |
##' @param fontsize size of text |
| ... | ... |
@@ -20,11 +21,21 @@ |
| 20 | 21 |
##' @return ggplot layers |
| 21 | 22 |
##' @export |
| 22 | 23 |
##' @author Guangchuang Yu |
| 23 |
-geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
|
| 24 |
- align=FALSE, barsize=0.5, fontsize=3.88, |
|
| 25 |
- angle=0, geom="text", hjust = 0, |
|
| 26 |
- color = NULL, fill=NA, |
|
| 27 |
- family="sans", parse=FALSE, ...) {
|
|
| 24 |
+geom_cladelabel <- function(node, label, |
|
| 25 |
+ offset = 0, |
|
| 26 |
+ offset.text = 0, |
|
| 27 |
+ extend = 0, |
|
| 28 |
+ align = FALSE, |
|
| 29 |
+ barsize = 0.5, |
|
| 30 |
+ fontsize = 3.88, |
|
| 31 |
+ angle = 0, |
|
| 32 |
+ geom = "text", |
|
| 33 |
+ hjust = 0, |
|
| 34 |
+ color = NULL, |
|
| 35 |
+ fill = NA, |
|
| 36 |
+ family = "sans", |
|
| 37 |
+ parse = FALSE, |
|
| 38 |
+ ...) {
|
|
| 28 | 39 |
mapping <- NULL |
| 29 | 40 |
data <- NULL |
| 30 | 41 |
position <- "identity" |
| ... | ... |
@@ -73,7 +84,7 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 73 | 84 |
} |
| 74 | 85 |
|
| 75 | 86 |
layer_bar <- stat_cladeBar(node=node, offset=offset, align=align, |
| 76 |
- size=barsize, |
|
| 87 |
+ size=barsize, extend = extend, |
|
| 77 | 88 |
mapping=mapping, data=data, |
| 78 | 89 |
position=position, show.legend = show.legend, |
| 79 | 90 |
inherit.aes = inherit.aes, na.rm=na.rm, ...) |
| ... | ... |
@@ -95,11 +106,18 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 95 | 106 |
parse = parse, ...) |
| 96 | 107 |
} |
| 97 | 108 |
|
| 98 |
- layer_bar <- stat_cladeBar(node=node, offset=offset, align=align, |
|
| 99 |
- size=barsize, color = barcolor, |
|
| 100 |
- mapping=mapping, data=data, |
|
| 101 |
- position=position, show.legend = show.legend, |
|
| 102 |
- inherit.aes = inherit.aes, na.rm=na.rm, ...) |
|
| 109 |
+ layer_bar <- stat_cladeBar(node = node, |
|
| 110 |
+ offset = offset, |
|
| 111 |
+ align = align, |
|
| 112 |
+ size = barsize, |
|
| 113 |
+ color = barcolor, |
|
| 114 |
+ extend = extend, |
|
| 115 |
+ mapping = mapping, |
|
| 116 |
+ data = data, |
|
| 117 |
+ position = position, |
|
| 118 |
+ show.legend = show.legend, |
|
| 119 |
+ inherit.aes = inherit.aes, |
|
| 120 |
+ na.rm = na.rm, ...) |
|
| 103 | 121 |
|
| 104 | 122 |
} |
| 105 | 123 |
|
| ... | ... |
@@ -110,11 +128,11 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 110 | 128 |
} |
| 111 | 129 |
|
| 112 | 130 |
|
| 113 |
-stat_cladeText <- function(mapping=NULL, data=NULL, |
|
| 114 |
- geom="text", position="identity", |
|
| 131 |
+stat_cladeText <- function(mapping = NULL, data = NULL, |
|
| 132 |
+ geom = "text", position = "identity", |
|
| 115 | 133 |
node, label, offset, align, ..., angle, |
| 116 |
- show.legend=NA, inherit.aes=FALSE, |
|
| 117 |
- na.rm=FALSE, parse=FALSE) {
|
|
| 134 |
+ show.legend = NA, inherit.aes = FALSE, |
|
| 135 |
+ na.rm = FALSE, parse = FALSE) {
|
|
| 118 | 136 |
default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, angle=~angle) |
| 119 | 137 |
if (is.null(mapping)) {
|
| 120 | 138 |
mapping <- default_aes |
| ... | ... |
@@ -122,14 +140,14 @@ stat_cladeText <- function(mapping=NULL, data=NULL, |
| 122 | 140 |
mapping <- modifyList(mapping, default_aes) |
| 123 | 141 |
} |
| 124 | 142 |
|
| 125 |
- layer(stat=StatCladeText, |
|
| 126 |
- data=data, |
|
| 127 |
- mapping=mapping, |
|
| 128 |
- geom=geom, |
|
| 129 |
- position=position, |
|
| 143 |
+ layer(stat = StatCladeText, |
|
| 144 |
+ data = data, |
|
| 145 |
+ mapping = mapping, |
|
| 146 |
+ geom = geom, |
|
| 147 |
+ position = position, |
|
| 130 | 148 |
show.legend = show.legend, |
| 131 | 149 |
inherit.aes = inherit.aes, |
| 132 |
- params=list(node=node, |
|
| 150 |
+ params=list(node = node, |
|
| 133 | 151 |
label = label, |
| 134 | 152 |
offset = offset, |
| 135 | 153 |
align = align, |
| ... | ... |
@@ -144,7 +162,7 @@ stat_cladeText <- function(mapping=NULL, data=NULL, |
| 144 | 162 |
|
| 145 | 163 |
stat_cladeBar <- function(mapping=NULL, data=NULL, |
| 146 | 164 |
geom="segment", position="identity", |
| 147 |
- node, offset, align, ..., |
|
| 165 |
+ node, offset, align, extend, ..., |
|
| 148 | 166 |
show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {
|
| 149 | 167 |
default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, xend=~x, yend=~y) |
| 150 | 168 |
if (is.null(mapping)) {
|
| ... | ... |
@@ -153,17 +171,18 @@ stat_cladeBar <- function(mapping=NULL, data=NULL, |
| 153 | 171 |
mapping <- modifyList(mapping, default_aes) |
| 154 | 172 |
} |
| 155 | 173 |
|
| 156 |
- layer(stat=StatCladeBar, |
|
| 157 |
- data=data, |
|
| 158 |
- mapping=mapping, |
|
| 159 |
- geom=geom, |
|
| 160 |
- position=position, |
|
| 174 |
+ layer(stat = StatCladeBar, |
|
| 175 |
+ data = data, |
|
| 176 |
+ mapping = mapping, |
|
| 177 |
+ geom = geom, |
|
| 178 |
+ position = position, |
|
| 161 | 179 |
show.legend = show.legend, |
| 162 | 180 |
inherit.aes = inherit.aes, |
| 163 |
- params=list(node=node, |
|
| 164 |
- offset=offset, |
|
| 165 |
- align=align, |
|
| 166 |
- na.rm=na.rm, |
|
| 181 |
+ params = list(node = node, |
|
| 182 |
+ offset = offset, |
|
| 183 |
+ extend = extend, |
|
| 184 |
+ align = align, |
|
| 185 |
+ na.rm = na.rm, |
|
| 167 | 186 |
...), |
| 168 | 187 |
check.aes = FALSE |
| 169 | 188 |
) |
| ... | ... |
@@ -182,15 +201,15 @@ StatCladeText <- ggproto("StatCladeText", Stat,
|
| 182 | 201 |
|
| 183 | 202 |
|
| 184 | 203 |
StatCladeBar <- ggproto("StatCladBar", Stat,
|
| 185 |
- compute_group = function(self, data, scales, params, node, offset, align) {
|
|
| 186 |
- get_cladelabel_position(data, node, offset, align, adjustRatio=1.02, angle=0) |
|
| 204 |
+ compute_group = function(self, data, scales, params, node, offset, align, extend) {
|
|
| 205 |
+ get_cladelabel_position(data, node, offset, align, adjustRatio=1.02, angle=0, extend=extend) |
|
| 187 | 206 |
}, |
| 188 | 207 |
required_aes = c("x", "y", "xend", "yend")
|
| 189 | 208 |
) |
| 190 | 209 |
|
| 191 | 210 |
|
| 192 |
-get_cladelabel_position <- function(data, node, offset, align, adjustRatio, angle="auto") {
|
|
| 193 |
- df <- get_cladelabel_position_(data, node, angle) |
|
| 211 |
+get_cladelabel_position <- function(data, node, offset, align, adjustRatio, angle="auto", extend=0) {
|
|
| 212 |
+ df <- get_cladelabel_position_(data, node, angle, extend) |
|
| 194 | 213 |
if (align) {
|
| 195 | 214 |
mx <- max(data$x, na.rm=TRUE) |
| 196 | 215 |
} else {
|
| ... | ... |
@@ -203,12 +222,12 @@ get_cladelabel_position <- function(data, node, offset, align, adjustRatio, angl |
| 203 | 222 |
## } |
| 204 | 223 |
|
| 205 | 224 |
mx <- mx * adjustRatio + offset |
| 206 |
- |
|
| 225 |
+ |
|
| 207 | 226 |
data.frame(x=mx, xend=mx, y=df$y, yend=df$yend, angle=angle) |
| 208 | 227 |
} |
| 209 | 228 |
|
| 210 | 229 |
|
| 211 |
-get_cladelabel_position_ <- function(data, node, angle="auto") {
|
|
| 230 |
+get_cladelabel_position_ <- function(data, node, angle = "auto", extend = 0) {
|
|
| 212 | 231 |
sp <- get.offspring.df(data, node) |
| 213 | 232 |
sp2 <- c(sp, node) |
| 214 | 233 |
sp.df <- data[match(sp2, data$node),] |
| ... | ... |
@@ -217,7 +236,7 @@ get_cladelabel_position_ <- function(data, node, angle="auto") {
|
| 217 | 236 |
y <- y[!is.na(y)] |
| 218 | 237 |
mx <- max(sp.df$x, na.rm=TRUE) |
| 219 | 238 |
|
| 220 |
- d <- data.frame(x=mx, y=min(y), yend=max(y)) |
|
| 239 |
+ d <- data.frame(x=mx, y=min(y) - extend, yend=max(y) + extend) |
|
| 221 | 240 |
if (missing(angle)) |
| 222 | 241 |
return(d) |
| 223 | 242 |
|
| ... | ... |
@@ -226,6 +245,7 @@ get_cladelabel_position_ <- function(data, node, angle="auto") {
|
| 226 | 245 |
} else {
|
| 227 | 246 |
d$angle <- angle |
| 228 | 247 |
} |
| 248 |
+ |
|
| 229 | 249 |
return(d) |
| 230 | 250 |
} |
| 231 | 251 |
|
| ... | ... |
@@ -6,7 +6,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with |
| 6 | 6 |
|
| 7 | 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) [](#backers) [](#sponsors) |
| 12 | 12 |
|
| ... | ... |
@@ -27,7 +27,7 @@ Please cite the following article when using `ggtree`: |
| 27 | 27 |
|
| 28 | 28 |
**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. |
| 29 | 29 |
|
| 30 |
-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 30 |
+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
|
| 31 | 31 |
|
| 32 | 32 |
------------------------------------------------------------------------ |
| 33 | 33 |
|
| ... | ... |
@@ -30,11 +30,10 @@ highlights the two direct descendant clades of an internal node |
| 30 | 30 |
Particularly useful when studying neighboring clades. Note that balances that |
| 31 | 31 |
correspond to multichotomies will not be displayed. |
| 32 | 32 |
} |
| 33 |
-\author{
|
|
| 34 |
-Justin Silverman |
|
| 35 |
-} |
|
| 36 | 33 |
\references{
|
| 37 | 34 |
J. Silverman, et al. \emph{A phylogenetic transform enhances
|
| 38 | 35 |
analysis of compositional microbiota data}. (in preparation) |
| 39 | 36 |
} |
| 40 |
- |
|
| 37 |
+\author{
|
|
| 38 |
+Justin Silverman |
|
| 39 |
+} |
| ... | ... |
@@ -4,9 +4,10 @@ |
| 4 | 4 |
\alias{geom_cladelabel}
|
| 5 | 5 |
\title{geom_cladelabel}
|
| 6 | 6 |
\usage{
|
| 7 |
-geom_cladelabel(node, label, offset = 0, offset.text = 0, align = FALSE, |
|
| 8 |
- barsize = 0.5, fontsize = 3.88, angle = 0, geom = "text", hjust = 0, |
|
| 9 |
- color = NULL, fill = NA, family = "sans", parse = FALSE, ...) |
|
| 7 |
+geom_cladelabel(node, label, offset = 0, offset.text = 0, extend = 0, |
|
| 8 |
+ align = FALSE, barsize = 0.5, fontsize = 3.88, angle = 0, |
|
| 9 |
+ geom = "text", hjust = 0, color = NULL, fill = NA, family = "sans", |
|
| 10 |
+ parse = FALSE, ...) |
|
| 10 | 11 |
} |
| 11 | 12 |
\arguments{
|
| 12 | 13 |
\item{node}{selected node}
|
| ... | ... |
@@ -17,6 +18,8 @@ geom_cladelabel(node, label, offset = 0, offset.text = 0, align = FALSE, |
| 17 | 18 |
|
| 18 | 19 |
\item{offset.text}{offset of text from bar}
|
| 19 | 20 |
|
| 21 |
+\item{extend}{extend bar height}
|
|
| 22 |
+ |
|
| 20 | 23 |
\item{align}{logical}
|
| 21 | 24 |
|
| 22 | 25 |
\item{barsize}{size of bar}
|
| ... | ... |
@@ -48,4 +51,3 @@ annotate a clade with bar and text label |
| 48 | 51 |
\author{
|
| 49 | 52 |
Guangchuang Yu |
| 50 | 53 |
} |
| 51 |
- |
| ... | ... |
@@ -18,4 +18,3 @@ named list of subtrees with the root id of subtree and list of node id's making |
| 18 | 18 |
Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree) |
| 19 | 19 |
return named list of subtrees with list name as starting node id. |
| 20 | 20 |
} |
| 21 |
- |
| ... | ... |
@@ -3,8 +3,9 @@ |
| 3 | 3 |
\docType{package}
|
| 4 | 4 |
\name{ggtree}
|
| 5 | 5 |
\alias{ggtree}
|
| 6 |
-\alias{ggtree-package}
|
|
| 7 | 6 |
\alias{package-ggtree}
|
| 7 |
+\alias{ggtree-package}
|
|
| 8 |
+\alias{ggtree}
|
|
| 8 | 9 |
\title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
|
| 9 | 10 |
\code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
|
| 10 | 11 |
\usage{
|
| ... | ... |
@@ -57,4 +58,3 @@ ggtree(tr) |
| 57 | 58 |
\author{
|
| 58 | 59 |
Yu Guangchuang |
| 59 | 60 |
} |
| 60 |
- |
| ... | ... |
@@ -3,12 +3,13 @@ |
| 3 | 3 |
\docType{methods}
|
| 4 | 4 |
\name{gzoom}
|
| 5 | 5 |
\alias{gzoom}
|
| 6 |
+\alias{gzoom}
|
|
| 7 |
+\alias{gzoom,ggtree-method}
|
|
| 6 | 8 |
\alias{gzoom,beast-method}
|
| 7 | 9 |
\alias{gzoom,codeml-method}
|
| 8 |
-\alias{gzoom,ggtree-method}
|
|
| 10 |
+\alias{gzoom,treedata-method}
|
|
| 9 | 11 |
\alias{gzoom,paml_rst-method}
|
| 10 | 12 |
\alias{gzoom,phylo-method}
|
| 11 |
-\alias{gzoom,treedata-method}
|
|
| 12 | 13 |
\title{gzoom method}
|
| 13 | 14 |
\usage{
|
| 14 | 15 |
gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...) |
| ... | ... |
@@ -50,4 +51,3 @@ figure |
| 50 | 51 |
\description{
|
| 51 | 52 |
zoom selected subtree |
| 52 | 53 |
} |
| 53 |
- |
| ... | ... |
@@ -4,9 +4,9 @@ |
| 4 | 4 |
\name{scale_color}
|
| 5 | 5 |
\alias{scale_color}
|
| 6 | 6 |
\alias{scale_color,beast-method}
|
| 7 |
+\alias{scale_color,treedata-method}
|
|
| 7 | 8 |
\alias{scale_color,paml_rst-method}
|
| 8 | 9 |
\alias{scale_color,phylo-method}
|
| 9 |
-\alias{scale_color,treedata-method}
|
|
| 10 | 10 |
\title{scale_color method}
|
| 11 | 11 |
\usage{
|
| 12 | 12 |
scale_color(object, by, ...) |
| ... | ... |
@@ -33,4 +33,3 @@ color vector |
| 33 | 33 |
\description{
|
| 34 | 34 |
scale color by a numerical tree attribute |
| 35 | 35 |
} |
| 36 |
- |
