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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 |
5 |
-Version: 1.13.0.005 |
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+Version: 1.13.0.006 |
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6 | 6 |
Authors@R: c( |
7 | 7 |
person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")), |
8 | 8 |
person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", role = c("aut", "ths")), |
... | ... |
@@ -29,7 +29,7 @@ Imports: |
29 | 29 |
scales, |
30 | 30 |
tibble, |
31 | 31 |
tidyr, |
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- tidytree (>= 0.1.5), |
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+ tidytree (>= 0.1.9), |
|
33 | 33 |
treeio (>= 1.3.14), |
34 | 34 |
utils |
35 | 35 |
Suggests: |
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@@ -1,5 +1,7 @@ |
1 |
-# ggtree 1.13.0.005 |
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+# ggtree 1.13.0.006 |
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2 | 2 |
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++ `geom_rootedge` (2018-06-13, Wed) |
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+ - <https://github.com/GuangchuangYu/ggtree/issues/183> |
|
3 | 5 |
+ `clade_name` parameter added in `collapse` (2018-05-28, Mon) |
4 | 6 |
- <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/0H1PCJPlI1Q/DeZf9EVhBQAJ> |
5 | 7 |
+ bug fixed of `gheatmap` for rowname subsetting is partial match in R |
6 | 8 |
new file mode 100644 |
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@@ -0,0 +1,44 @@ |
1 |
+##' display root edge |
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+##' |
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+##' |
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+##' @title geom_rootedge |
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+##' @param rootedge length of rootedge; use phylo$root.edge if rootedge = NULL (by default). |
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+##' @return ggplot layer |
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+##' @export |
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+##' @author Guangchuang Yu |
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+geom_rootedge <- function(rootedge = NULL) { |
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+ mapping <- aes_(x = ~x, y = ~y, xend = ~x, yend = ~y, |
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+ branch.length = ~branch.length, |
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+ node = ~node, parent = ~parent) |
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+ layer( |
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+ stat = StatRootEdge, |
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+ data = NULL, |
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+ mapping = mapping, |
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+ geom = "segment", |
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+ position = "identity", |
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+ show.legend = NA, |
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+ params = list(rootedge = rootedge), |
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+ check.aes = FALSE |
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+ ) |
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+ |
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+} |
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+ |
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+ |
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27 |
+ |
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+StatRootEdge <- ggproto("StatRootEdge", Stat, |
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+ compute_group = function(self, data, scales, params, rootedge) { |
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+ d <- data[data$parent == data$node,] |
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+ if (is.null(rootedge)) { |
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32 |
+ rootedge <- d$branch.length |
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33 |
+ } |
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+ if (is.null(rootedge) || is.na(rootedge)) { |
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+ xend <- d$x |
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+ } else { |
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+ xend <- -rootedge |
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+ } |
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+ |
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+ data.frame(x = d$x, y = d$y, |
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+ xend = xend, yend = d$y) |
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+ }, |
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+ required_aes = c("x", "y", "xend", "yend") |
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+ ) |
0 | 45 |
new file mode 100644 |
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@@ -0,0 +1,20 @@ |
1 |
+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/geom_rootedge.R |
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+\name{geom_rootedge} |
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+\alias{geom_rootedge} |
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+\title{geom_rootedge} |
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+\usage{ |
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+geom_rootedge(rootedge = NULL) |
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+} |
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+\arguments{ |
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+\item{rootedge}{length of rootedge; use phylo$root.edge if rootedge = NULL (by default).} |
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+} |
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+\value{ |
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+ggplot layer |
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+} |
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+\description{ |
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+display root edge |
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+} |
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+\author{ |
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+Guangchuang Yu |
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+} |