GuangchuangYu authored on 05/05/2017 21:01:50
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@@ -2,7 +2,7 @@ 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 |
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-Version: 1.9.0 |
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+Version: 1.9.1 |
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| 6 | 6 |
Authors@R: c( |
| 7 | 7 |
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
|
| 8 | 8 |
person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
|
| ... | ... |
@@ -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 |
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-RoxygenNote: 5.0.1 |
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+RoxygenNote: 6.0.1 |
| ... | ... |
@@ -69,7 +69,7 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 69 | 69 |
mapping=mapping, data=data, geom=geom, hjust=hjust, |
| 70 | 70 |
position=position, show.legend = show.legend, |
| 71 | 71 |
inherit.aes = inherit.aes, na.rm=na.rm, |
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- parse = parse, ...) |
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+ parse = parse, ...) |
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| 73 | 73 |
} |
| 74 | 74 |
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| 75 | 75 |
layer_bar <- stat_cladeBar(node=node, offset=offset, align=align, |
| ... | ... |
@@ -84,7 +84,7 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 84 | 84 |
align=align, size=fontsize, angle=angle, color=labelcolor, family=family, |
| 85 | 85 |
mapping=mapping, data=data, geom=geom, hjust=hjust, |
| 86 | 86 |
position=position, show.legend = show.legend, |
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- inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...) |
|
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+ inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...) |
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| 88 | 88 |
|
| 89 | 89 |
} else {
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| 90 | 90 |
layer_text = stat_cladeText(node=node, label=label, offset=offset+offset.text, |
| ... | ... |
@@ -92,7 +92,7 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 92 | 92 |
mapping=mapping, data=data, geom=geom, hjust=hjust, |
| 93 | 93 |
position=position, show.legend = show.legend, |
| 94 | 94 |
inherit.aes = inherit.aes, na.rm=na.rm, |
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- parse = parse, ...) |
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+ parse = parse, ...) |
|
| 96 | 96 |
} |
| 97 | 97 |
|
| 98 | 98 |
layer_bar <- stat_cladeBar(node=node, offset=offset, align=align, |
| ... | ... |
@@ -112,10 +112,10 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0, |
| 112 | 112 |
|
| 113 | 113 |
stat_cladeText <- function(mapping=NULL, data=NULL, |
| 114 | 114 |
geom="text", position="identity", |
| 115 |
- node, label, offset, align, ..., |
|
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+ node, label, offset, align, ..., angle, |
|
| 116 | 116 |
show.legend=NA, inherit.aes=FALSE, |
| 117 | 117 |
na.rm=FALSE, parse=FALSE) {
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- default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent) |
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+ default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, angle=~angle) |
|
| 119 | 119 |
if (is.null(mapping)) {
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| 120 | 120 |
mapping <- default_aes |
| 121 | 121 |
} else {
|
| ... | ... |
@@ -135,6 +135,7 @@ stat_cladeText <- function(mapping=NULL, data=NULL, |
| 135 | 135 |
align = align, |
| 136 | 136 |
na.rm = na.rm, |
| 137 | 137 |
parse = parse, |
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+ angle_ = angle, |
|
| 138 | 139 |
...), |
| 139 | 140 |
check.aes = FALSE |
| 140 | 141 |
) |
| ... | ... |
@@ -169,38 +170,45 @@ stat_cladeBar <- function(mapping=NULL, data=NULL, |
| 169 | 170 |
} |
| 170 | 171 |
|
| 171 | 172 |
StatCladeText <- ggproto("StatCladeText", Stat,
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- compute_group = function(self, data, scales, params, node, label, offset, align) {
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- df <- get_cladelabel_position(data, node, offset, align, adjustRatio = 1.03) |
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+ compute_group = function(self, data, scales, params, node, label, offset, align, angle_) {
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+ df <- get_cladelabel_position(data, node, offset, align, adjustRatio = 1.03, angle_) |
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| 174 | 175 |
df$y <- mean(c(df$y, df$yend)) |
| 175 | 176 |
df$label <- label |
| 176 | 177 |
return(df) |
| 177 | 178 |
}, |
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- required_aes = c("x", "y", "label")
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+ required_aes = c("x", "y", "label", "angle")
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| 179 | 180 |
) |
| 180 | 181 |
|
| 181 | 182 |
|
| 182 | 183 |
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| 183 | 184 |
StatCladeBar <- ggproto("StatCladBar", Stat,
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| 184 | 185 |
compute_group = function(self, data, scales, params, node, offset, align) {
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- get_cladelabel_position(data, node, offset, align, adjustRatio=1.02) |
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+ get_cladelabel_position(data, node, offset, align, adjustRatio=1.02, angle=0) |
|
| 186 | 187 |
}, |
| 187 | 188 |
required_aes = c("x", "y", "xend", "yend")
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| 188 | 189 |
) |
| 189 | 190 |
|
| 190 | 191 |
|
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-get_cladelabel_position <- function(data, node, offset, align, adjustRatio) {
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- df <- get_cladelabel_position_(data, node) |
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+get_cladelabel_position <- function(data, node, offset, align, adjustRatio, angle="auto") {
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+ df <- get_cladelabel_position_(data, node, angle) |
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| 193 | 194 |
if (align) {
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| 194 | 195 |
mx <- max(data$x, na.rm=TRUE) |
| 195 | 196 |
} else {
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| 196 | 197 |
mx <- df$x |
| 197 | 198 |
} |
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+ |
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+ angle <- df$angle |
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+ ## if (angle >= 90 & angle <=270) {
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+ ## angle <- angle + 180 |
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+ ## } |
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+ |
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mx <- mx * adjustRatio + offset |
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- data.frame(x=mx, xend=mx, y=df$y, yend=df$yend) |
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+ |
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+ data.frame(x=mx, xend=mx, y=df$y, yend=df$yend, angle=angle) |
|
| 200 | 208 |
} |
| 201 | 209 |
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| 202 | 210 |
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-get_cladelabel_position_ <- function(data, node) {
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+get_cladelabel_position_ <- function(data, node, angle="auto") {
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| 204 | 212 |
sp <- get.offspring.df(data, node) |
| 205 | 213 |
sp2 <- c(sp, node) |
| 206 | 214 |
sp.df <- data[match(sp2, data$node),] |
| ... | ... |
@@ -208,6 +216,16 @@ get_cladelabel_position_ <- function(data, node) {
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| 208 | 216 |
y <- sp.df$y |
| 209 | 217 |
y <- y[!is.na(y)] |
| 210 | 218 |
mx <- max(sp.df$x, na.rm=TRUE) |
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- data.frame(x=mx, y=min(y), yend=max(y)) |
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+ |
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+ d <- data.frame(x=mx, y=min(y), yend=max(y)) |
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+ if (missing(angle)) |
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+ return(d) |
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+ |
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+ if (angle == "auto") {
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+ d$angle <- mean(range(sp.df$angle)) |
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+ } else {
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+ d$angle <- angle |
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+ } |
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+ return(d) |
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} |
| 213 | 231 |
|
| ... | ... |
@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with |
| 4 | 4 |
|
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<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /> |
| 6 | 6 |
|
| 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) |
|
| 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 |
|
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-[](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 |
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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) |
| 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) |
|
| 30 |
+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) |
|
| 31 | 31 |
|
| 32 | 32 |
------------------------------------------------------------------------ |
| 33 | 33 |
|
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@@ -53,30 +53,30 @@ Please cite the following article when using `ggtree`: |
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|
| 54 | 54 |
### Download stats |
| 55 | 55 |
|
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-[](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 |
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- ++-------------------+------------------+-------------------+------------------+--------------+ |
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- 3000 + * + |
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+ ++------------------+------------------+------------------+-----------------+-----------------+ |
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+ 3000 + * + |
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| | |
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| | |
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2500 + + |
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| | |
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- 2000 + + |
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- | * * * | |
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- | * * | |
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+ 2000 + * + |
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+ | * * * | |
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+ | * * | |
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1500 + + |
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| | |
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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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- 500 + * * + |
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- | * * | |
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- | * | |
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- 0 + * * * + |
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- ++-------------------+------------------+-------------------+------------------+--------------+ |
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- 2015 2015.5 2016 2016.5 2017 |
|
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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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+ 500 + * * + |
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+ | * * | |
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+ | * | |
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+ 0 + * * * + |
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+ ++------------------+------------------+------------------+-----------------+-----------------+ |
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+ 2015 2015.5 2016 2016.5 2017 |
| ... | ... |
@@ -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 |
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correspond to multichotomies will not be displayed. |
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} |
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-\author{
|
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-Justin Silverman |
|
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-} |
|
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\references{
|
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J. Silverman, et al. \emph{A phylogenetic transform enhances
|
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analysis of compositional microbiota data}. (in preparation) |
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} |
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- |
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+\author{
|
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+Justin Silverman |
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+} |
| ... | ... |
@@ -18,4 +18,3 @@ named list of subtrees with the root id of subtree and list of node id's making |
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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 |
} |
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- |
| ... | ... |
@@ -3,8 +3,9 @@ |
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\docType{package}
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\name{ggtree}
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\alias{ggtree}
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-\alias{ggtree-package}
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\alias{package-ggtree}
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+\alias{ggtree-package}
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+\alias{ggtree}
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\title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
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\code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
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\usage{
|
| ... | ... |
@@ -57,4 +58,3 @@ ggtree(tr) |
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\author{
|
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Yu Guangchuang |
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} |
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- |
| ... | ... |
@@ -3,12 +3,13 @@ |
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\docType{methods}
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\name{gzoom}
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\alias{gzoom}
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+\alias{gzoom}
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+\alias{gzoom,ggtree-method}
|
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\alias{gzoom,beast-method}
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\alias{gzoom,codeml-method}
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-\alias{gzoom,ggtree-method}
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+\alias{gzoom,treedata-method}
|
|
| 9 | 11 |
\alias{gzoom,paml_rst-method}
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\alias{gzoom,phylo-method}
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-\alias{gzoom,treedata-method}
|
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\title{gzoom method}
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\usage{
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gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...) |
| ... | ... |
@@ -50,4 +51,3 @@ figure |
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\description{
|
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zoom selected subtree |
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} |
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- |
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@@ -4,9 +4,9 @@ |
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\name{scale_color}
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\alias{scale_color}
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\alias{scale_color,beast-method}
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+\alias{scale_color,treedata-method}
|
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\alias{scale_color,paml_rst-method}
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\alias{scale_color,phylo-method}
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-\alias{scale_color,treedata-method}
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\title{scale_color method}
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\usage{
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scale_color(object, by, ...) |
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@@ -33,4 +33,3 @@ color vector |
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\description{
|
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scale color by a numerical tree attribute |
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} |
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- |