... | ... |
@@ -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: 1.13.2 |
|
5 |
+Version: 1.13.3 |
|
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")), |
... | ... |
@@ -51,4 +51,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues |
51 | 51 |
Packaged: 2014-12-03 08:16:14 UTC; root |
52 | 52 |
biocViews: Alignment, Annotation, Clustering, DataImport, |
53 | 53 |
MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization |
54 |
-RoxygenNote: 6.0.1 |
|
54 |
+RoxygenNote: 6.1.0 |
... | ... |
@@ -40,7 +40,7 @@ viewClade <- function(tree_view=NULL, node, xmax_adjust=0) { |
40 | 40 |
## xd <- tree_view$data$branch.length[node]/2 |
41 | 41 |
|
42 | 42 |
cpos <- get_clade_position(tree_view, node=node) |
43 |
- xmax <- ggplot_build(tree_view)$layout$panel_ranges[[1]]$x.range[2] |
|
43 |
+ xmax <- ggplot_build(tree_view)$layout$panel_params[[1]]$x.range[2] |
|
44 | 44 |
|
45 | 45 |
attr(tree_view, 'viewClade') <- TRUE |
46 | 46 |
attr(tree_view, 'viewClade_node') <- node |
... | ... |
@@ -6,8 +6,8 @@ |
6 | 6 |
\usage{ |
7 | 7 |
geom_cladelabel(node, label, offset = 0, offset.text = 0, extend = 0, |
8 | 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, ...) |
|
9 |
+ geom = "text", hjust = 0, color = NULL, fill = NA, |
|
10 |
+ family = "sans", parse = FALSE, ...) |
|
11 | 11 |
} |
12 | 12 |
\arguments{ |
13 | 13 |
\item{node}{selected node} |
... | ... |
@@ -4,9 +4,10 @@ |
4 | 4 |
\alias{geom_cladelabel2} |
5 | 5 |
\title{geom_cladelabel2} |
6 | 6 |
\usage{ |
7 |
-geom_cladelabel2(node, label, offset = 0, offset.text = 0, offset.bar = 0, |
|
8 |
- align = FALSE, barsize = 0.5, fontsize = 3.88, hjust = 0, |
|
9 |
- geom = "text", color = NULL, family = "sans", parse = FALSE, ...) |
|
7 |
+geom_cladelabel2(node, label, offset = 0, offset.text = 0, |
|
8 |
+ offset.bar = 0, align = FALSE, barsize = 0.5, fontsize = 3.88, |
|
9 |
+ hjust = 0, geom = "text", color = NULL, family = "sans", |
|
10 |
+ parse = FALSE, ...) |
|
10 | 11 |
} |
11 | 12 |
\arguments{ |
12 | 13 |
\item{node}{selected node} |
... | ... |
@@ -5,10 +5,10 @@ |
5 | 5 |
\title{geom_label2} |
6 | 6 |
\usage{ |
7 | 7 |
geom_label2(mapping = NULL, data = NULL, ..., stat = "identity", |
8 |
- position = "identity", family = "sans", parse = FALSE, nudge_x = 0, |
|
9 |
- nudge_y = 0, label.padding = unit(0.25, "lines"), label.r = unit(0.15, |
|
10 |
- "lines"), label.size = 0.25, na.rm = TRUE, show.legend = NA, |
|
11 |
- inherit.aes = TRUE) |
|
8 |
+ position = "identity", family = "sans", parse = FALSE, |
|
9 |
+ nudge_x = 0, nudge_y = 0, label.padding = unit(0.25, "lines"), |
|
10 |
+ label.r = unit(0.15, "lines"), label.size = 0.25, na.rm = TRUE, |
|
11 |
+ show.legend = NA, inherit.aes = TRUE) |
|
12 | 12 |
} |
13 | 13 |
\arguments{ |
14 | 14 |
\item{mapping}{the aesthetic mapping} |
... | ... |
@@ -4,8 +4,8 @@ |
4 | 4 |
\alias{geom_nodelab} |
5 | 5 |
\title{geom_nodelab} |
6 | 6 |
\usage{ |
7 |
-geom_nodelab(mapping = NULL, nudge_x = 0, nudge_y = 0, geom = "text", |
|
8 |
- hjust = 0.5, ...) |
|
7 |
+geom_nodelab(mapping = NULL, nudge_x = 0, nudge_y = 0, |
|
8 |
+ geom = "text", hjust = 0.5, ...) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{mapping}{aes mapping} |
... | ... |
@@ -4,8 +4,8 @@ |
4 | 4 |
\alias{geom_nodelab2} |
5 | 5 |
\title{@geom_nodelab2} |
6 | 6 |
\usage{ |
7 |
-geom_nodelab2(mapping = NULL, nudge_x = 0, nudge_y = 0, geom = "text", |
|
8 |
- hjust = 0.5, ...) |
|
7 |
+geom_nodelab2(mapping = NULL, nudge_x = 0, nudge_y = 0, |
|
8 |
+ geom = "text", hjust = 0.5, ...) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{mapping}{aes mapping} |
... | ... |
@@ -4,7 +4,8 @@ |
4 | 4 |
\alias{geom_range} |
5 | 5 |
\title{geom_range} |
6 | 6 |
\usage{ |
7 |
-geom_range(range = "length_0.95_HPD", branch.length = "branch.length", ...) |
|
7 |
+geom_range(range = "length_0.95_HPD", branch.length = "branch.length", |
|
8 |
+ ...) |
|
8 | 9 |
} |
9 | 10 |
\arguments{ |
10 | 11 |
\item{range}{range, e.g. "height_0.95_HPD"} |
... | ... |
@@ -5,9 +5,9 @@ |
5 | 5 |
\title{geom_strip} |
6 | 6 |
\usage{ |
7 | 7 |
geom_strip(taxa1, taxa2, label = NA, offset = 0, offset.text = 0, |
8 |
- align = TRUE, barsize = 0.5, extend = 0, fontsize = 3.88, angle = 0, |
|
9 |
- geom = "text", hjust = 0, fill = NA, family = "sans", parse = FALSE, |
|
10 |
- ...) |
|
8 |
+ align = TRUE, barsize = 0.5, extend = 0, fontsize = 3.88, |
|
9 |
+ angle = 0, geom = "text", hjust = 0, fill = NA, |
|
10 |
+ family = "sans", parse = FALSE, ...) |
|
11 | 11 |
} |
12 | 12 |
\arguments{ |
13 | 13 |
\item{taxa1}{taxa1} |
... | ... |
@@ -5,9 +5,9 @@ |
5 | 5 |
\title{geom_text2} |
6 | 6 |
\usage{ |
7 | 7 |
geom_text2(mapping = NULL, data = NULL, ..., stat = "identity", |
8 |
- position = "identity", family = "sans", parse = FALSE, na.rm = TRUE, |
|
9 |
- show.legend = NA, inherit.aes = TRUE, nudge_x = 0, nudge_y = 0, |
|
10 |
- check_overlap = FALSE) |
|
8 |
+ position = "identity", family = "sans", parse = FALSE, |
|
9 |
+ na.rm = TRUE, show.legend = NA, inherit.aes = TRUE, nudge_x = 0, |
|
10 |
+ nudge_y = 0, check_overlap = FALSE) |
|
11 | 11 |
} |
12 | 12 |
\arguments{ |
13 | 13 |
\item{mapping}{the aesthetic mapping} |
... | ... |
@@ -5,7 +5,8 @@ |
5 | 5 |
\title{geom_tiplab} |
6 | 6 |
\usage{ |
7 | 7 |
geom_tiplab(mapping = NULL, hjust = 0, align = FALSE, |
8 |
- linetype = "dotted", linesize = 0.5, geom = "text", offset = 0, ...) |
|
8 |
+ linetype = "dotted", linesize = 0.5, geom = "text", offset = 0, |
|
9 |
+ ...) |
|
9 | 10 |
} |
10 | 11 |
\arguments{ |
11 | 12 |
\item{mapping}{aes mapping} |
... | ... |
@@ -5,7 +5,8 @@ |
5 | 5 |
\title{geom_treescale} |
6 | 6 |
\usage{ |
7 | 7 |
geom_treescale(x = NULL, y = NULL, width = NULL, offset = NULL, |
8 |
- color = "black", linesize = 0.5, fontsize = 3.88, family = "sans") |
|
8 |
+ color = "black", linesize = 0.5, fontsize = 3.88, |
|
9 |
+ family = "sans") |
|
9 | 10 |
} |
10 | 11 |
\arguments{ |
11 | 12 |
\item{x}{x position} |
... | ... |
@@ -5,13 +5,13 @@ |
5 | 5 |
\alias{ggtree} |
6 | 6 |
\alias{package-ggtree} |
7 | 7 |
\alias{ggtree-package} |
8 |
-\alias{ggtree} |
|
9 | 8 |
\title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics |
10 | 9 |
\code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.} |
11 | 10 |
\usage{ |
12 | 11 |
ggtree(tr, mapping = NULL, layout = "rectangular", open.angle = 0, |
13 |
- mrsd = NULL, as.Date = FALSE, yscale = "none", yscale_mapping = NULL, |
|
14 |
- ladderize = TRUE, right = FALSE, branch.length = "branch.length", ...) |
|
12 |
+ mrsd = NULL, as.Date = FALSE, yscale = "none", |
|
13 |
+ yscale_mapping = NULL, ladderize = TRUE, right = FALSE, |
|
14 |
+ branch.length = "branch.length", ...) |
|
15 | 15 |
} |
16 | 16 |
\arguments{ |
17 | 17 |
\item{tr}{phylo object} |
... | ... |
@@ -4,9 +4,10 @@ |
4 | 4 |
\alias{gheatmap} |
5 | 5 |
\title{gheatmap} |
6 | 6 |
\usage{ |
7 |
-gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red", |
|
8 |
- color = "white", colnames = TRUE, colnames_position = "bottom", |
|
9 |
- colnames_angle = 0, colnames_level = NULL, colnames_offset_x = 0, |
|
7 |
+gheatmap(p, data, offset = 0, width = 1, low = "green", |
|
8 |
+ high = "red", color = "white", colnames = TRUE, |
|
9 |
+ colnames_position = "bottom", colnames_angle = 0, |
|
10 |
+ colnames_level = NULL, colnames_offset_x = 0, |
|
10 | 11 |
colnames_offset_y = 0, font.size = 4, hjust = 0.5) |
11 | 12 |
} |
12 | 13 |
\arguments{ |
... | ... |
@@ -3,7 +3,6 @@ |
3 | 3 |
\docType{methods} |
4 | 4 |
\name{gzoom} |
5 | 5 |
\alias{gzoom} |
6 |
-\alias{gzoom} |
|
7 | 6 |
\alias{gzoom,ggtree-method} |
8 | 7 |
\alias{gzoom,treedata-method} |
9 | 8 |
\alias{gzoom,phylo-method} |
... | ... |
@@ -14,8 +13,8 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...) |
14 | 13 |
\S4method{gzoom}{ggtree}(object, focus, widths = c(0.3, 0.7), |
15 | 14 |
xmax_adjust = 0) |
16 | 15 |
|
17 |
-\S4method{gzoom}{treedata}(object, focus, subtree = FALSE, widths = c(0.3, |
|
18 |
- 0.7)) |
|
16 |
+\S4method{gzoom}{treedata}(object, focus, subtree = FALSE, |
|
17 |
+ widths = c(0.3, 0.7)) |
|
19 | 18 |
|
20 | 19 |
\S4method{gzoom}{phylo}(object, focus, subtree = FALSE, widths = c(0.3, |
21 | 20 |
0.7)) |
... | ... |
@@ -37,5 +36,9 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...) |
37 | 36 |
figure |
38 | 37 |
} |
39 | 38 |
\description{ |
39 |
+gzoom method |
|
40 |
+ |
|
41 |
+gzoom method |
|
42 |
+ |
|
40 | 43 |
zoom selected subtree |
41 | 44 |
} |
... | ... |
@@ -4,8 +4,8 @@ |
4 | 4 |
\alias{inset} |
5 | 5 |
\title{inset} |
6 | 6 |
\usage{ |
7 |
-inset(tree_view, insets, width, height, hjust = 0, vjust = 0, x = "node", |
|
8 |
- reverse_x = FALSE, reverse_y = FALSE) |
|
7 |
+inset(tree_view, insets, width, height, hjust = 0, vjust = 0, |
|
8 |
+ x = "node", reverse_x = FALSE, reverse_y = FALSE) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{tree_view}{tree view} |
... | ... |
@@ -4,8 +4,8 @@ |
4 | 4 |
\alias{msaplot} |
5 | 5 |
\title{msaplot} |
6 | 6 |
\usage{ |
7 |
-msaplot(p, fasta, offset = 0, width = 1, color = NULL, window = NULL, |
|
8 |
- bg_line = TRUE, height = 0.8) |
|
7 |
+msaplot(p, fasta, offset = 0, width = 1, color = NULL, |
|
8 |
+ window = NULL, bg_line = TRUE, height = 0.8) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{p}{tree view} |
... | ... |
@@ -4,8 +4,8 @@ |
4 | 4 |
\alias{phylopic} |
5 | 5 |
\title{phylopic} |
6 | 6 |
\usage{ |
7 |
-phylopic(tree_view, phylopic_id, size = 512, color = "black", alpha = 0.5, |
|
8 |
- node = NULL, x = NULL, y = NULL, width = 0.1) |
|
7 |
+phylopic(tree_view, phylopic_id, size = 512, color = "black", |
|
8 |
+ alpha = 0.5, node = NULL, x = NULL, y = NULL, width = 0.1) |
|
9 | 9 |
} |
10 | 10 |
\arguments{ |
11 | 11 |
\item{tree_view}{tree view} |
... | ... |
@@ -4,67 +4,35 @@ |
4 | 4 |
\name{reexports} |
5 | 5 |
\alias{reexports} |
6 | 6 |
\alias{rtree} |
7 |
-\alias{reexports} |
|
8 | 7 |
\alias{read.tree} |
9 |
-\alias{reexports} |
|
10 | 8 |
\alias{read.nexus} |
11 |
-\alias{reexports} |
|
12 | 9 |
\alias{groupOTU} |
13 |
-\alias{reexports} |
|
14 | 10 |
\alias{groupClade} |
15 |
-\alias{reexports} |
|
16 | 11 |
\alias{collapse} |
17 |
-\alias{reexports} |
|
18 | 12 |
\alias{fortify} |
19 |
-\alias{reexports} |
|
20 | 13 |
\alias{ggplot} |
21 |
-\alias{reexports} |
|
22 | 14 |
\alias{xlim} |
23 |
-\alias{reexports} |
|
24 | 15 |
\alias{theme} |
25 |
-\alias{reexports} |
|
26 | 16 |
\alias{ggsave} |
27 |
-\alias{reexports} |
|
28 | 17 |
\alias{aes} |
29 |
-\alias{reexports} |
|
30 |
-\alias{fortify} |
|
31 |
-\alias{reexports} |
|
32 | 18 |
\alias{geom_text} |
33 |
-\alias{reexports} |
|
34 | 19 |
\alias{geom_label} |
35 |
-\alias{reexports} |
|
36 | 20 |
\alias{geom_point} |
37 |
-\alias{reexports} |
|
38 | 21 |
\alias{read.astral} |
39 |
-\alias{reexports} |
|
40 | 22 |
\alias{read.beast} |
41 |
-\alias{reexports} |
|
42 | 23 |
\alias{read.codeml} |
43 |
-\alias{reexports} |
|
44 | 24 |
\alias{read.codeml_mlc} |
45 |
-\alias{reexports} |
|
46 | 25 |
\alias{read.hyphy} |
47 |
-\alias{reexports} |
|
48 | 26 |
\alias{read.iqtree} |
49 |
-\alias{reexports} |
|
50 | 27 |
\alias{read.jplace} |
51 |
-\alias{reexports} |
|
52 | 28 |
\alias{read.jtree} |
53 |
-\alias{reexports} |
|
54 | 29 |
\alias{read.mrbayes} |
55 |
-\alias{reexports} |
|
56 | 30 |
\alias{read.newick} |
57 |
-\alias{reexports} |
|
58 | 31 |
\alias{read.nhx} |
59 |
-\alias{reexports} |
|
60 | 32 |
\alias{read.paml_rst} |
61 |
-\alias{reexports} |
|
62 | 33 |
\alias{read.phylip} |
63 |
-\alias{reexports} |
|
64 | 34 |
\alias{read.phyloT} |
65 |
-\alias{reexports} |
|
66 | 35 |
\alias{read.r8s} |
67 |
-\alias{reexports} |
|
68 | 36 |
\alias{read.raxml} |
69 | 37 |
\title{Objects exported from other packages} |
70 | 38 |
\keyword{internal} |