guangchuang yu authored on 29/06/2017 05:10:11 | ... | ... |
@@ -2,7 +2,7 @@ Package: ggtree |
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Type: Package |
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Title: an R package for visualization and annotation of phylogenetic trees with |
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their covariates and other associated data |
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-Version: 1.9.1 |
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+Version: 1.9.2 |
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Authors@R: c( |
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person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
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person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
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@@ -43,4 +43,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues |
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Packaged: 2014-12-03 08:16:14 UTC; root |
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biocViews: Alignment, Annotation, Clustering, DataImport, |
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MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization |
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-RoxygenNote: 6.0.1 |
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+RoxygenNote: 5.0.1 |
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@@ -1,3 +1,8 @@ |
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+CHANGES IN VERSION 1.9.2 |
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+------------------------ |
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+ o gheatmap support handling collapsed tree <2017-06-29, Thu> |
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+ + https://github.com/GuangchuangYu/ggtree/issues/137 |
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+ |
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CHANGES IN VERSION 1.9.1 |
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------------------------ |
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o now mapping parameter will passed to segment layer in geom_tiplab(align=T) <2017-06-19, Mon> |
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@@ -40,17 +40,23 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color= |
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## } |
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## convert width to width of each cell |
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- width <- width * (p$data$x %>% range %>% diff) / ncol(data) |
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+ width <- width * (p$data$x %>% range(na.rm=TRUE) %>% diff) / ncol(data) |
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isTip <- x <- y <- variable <- value <- from <- to <- NULL |
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df <- p$data |
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df <- df[df$isTip,] |
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- start <- max(df$x) + offset |
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+ start <- max(df$x, na.rm=TRUE) + offset |
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dd <- as.data.frame(data) |
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## dd$lab <- rownames(dd) |
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- lab <- df$label[order(df$y)] |
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+ i <- order(df$y) |
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+ |
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+ ## handle collapsed tree |
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+ ## https://github.com/GuangchuangYu/ggtree/issues/137 |
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+ i <- i[!is.na(df$y[i])] |
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+ |
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+ lab <- df$label[i] |
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dd <- dd[lab, , drop=FALSE] |
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dd$y <- sort(df$y) |
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dd$lab <- lab |
| ... | ... |
@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with |
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|
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<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /> |
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|
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-[](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) |
|
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+[](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) |
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|
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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) |
|
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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) |
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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) |
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|
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@@ -27,7 +27,7 @@ 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***. 2017, 8(1):28-36. |
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|
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-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) |
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+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) |
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------------------------------------------------------------------------ |
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|
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@@ -53,7 +53,7 @@ Please cite the following article when using `ggtree`: |
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|
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### Download stats |
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|
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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) |
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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) |
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++------------------+-----------------+-----------------+-----------------+------------------++ |
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3000 + * + |
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@@ -30,10 +30,11 @@ highlights the two direct descendant clades of an internal node |
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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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-\author{
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-Justin Silverman |
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-} |
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+ |
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@@ -19,9 +19,10 @@ tip label layer |
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\description{
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add tip label for circular layout |
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} |
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-\references{
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-\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
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-} |
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\author{
|
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Guangchuang Yu |
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} |
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+\references{
|
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+\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
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+} |
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+ |
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@@ -18,3 +18,4 @@ 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) |
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return named list of subtrees with list name as starting node id. |
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} |
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+ |
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@@ -3,9 +3,8 @@ |
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\docType{package}
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\name{ggtree}
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\alias{ggtree}
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-\alias{package-ggtree}
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\alias{ggtree-package}
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-\alias{ggtree}
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+\alias{package-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{
|
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@@ -58,3 +57,4 @@ ggtree(tr) |
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\author{
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Yu Guangchuang |
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} |
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+ |
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@@ -3,13 +3,12 @@ |
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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,treedata-method}
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+\alias{gzoom,ggtree-method}
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\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), ...) |
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@@ -51,3 +50,4 @@ 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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@@ -33,3 +33,4 @@ 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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+ |