... | ... |
@@ -1,7 +1,7 @@ |
1 | 1 |
Package: ggtree |
2 | 2 |
Type: Package |
3 | 3 |
Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
4 |
-Version: 1.7.0 |
|
4 |
+Version: 1.7.1 |
|
5 | 5 |
Author: Guangchuang Yu and Tommy Tsan-Yuk Lam |
6 | 6 |
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com> |
7 | 7 |
Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. |
... | ... |
@@ -1,7 +1,11 @@ |
1 |
+CHANGES IN VERSION 1.7.1 |
|
2 |
+------------------------ |
|
3 |
+ o make tree stats available in facet_plot <2016-10-24, Mon> |
|
4 |
+ |
|
1 | 5 |
CHANGES IN VERSION 1.6.0 |
2 | 6 |
------------------------ |
3 | 7 |
o BioC 3.4 released <2016-10-18, Tue> |
4 |
- |
|
8 |
+ |
|
5 | 9 |
CHANGES IN VERSION 1.5.17 |
6 | 10 |
------------------------ |
7 | 11 |
o read.nhx support newick file <2016-10-17, Mon> |
... | ... |
@@ -1,4 +1,4 @@ |
1 |
-##' update tree |
|
1 |
+##' update tree |
|
2 | 2 |
##' |
3 | 3 |
##' |
4 | 4 |
##' @rdname update-TREE |
... | ... |
@@ -34,8 +34,8 @@ |
34 | 34 |
##' @examples |
35 | 35 |
##' nwk <- system.file("extdata", "sample.nwk", package="ggtree") |
36 | 36 |
##' tree <- read.tree(nwk) |
37 |
-##' p <- ggtree(tree) |
|
38 |
-##' dd <- data.frame(taxa=LETTERS[1:13], |
|
37 |
+##' p <- ggtree(tree) |
|
38 |
+##' dd <- data.frame(taxa=LETTERS[1:13], |
|
39 | 39 |
##' place=c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA), |
40 | 40 |
##' value=round(abs(rnorm(13, mean=70, sd=10)), digits=1)) |
41 | 41 |
##' row.names(dd) <- NULL |
... | ... |
@@ -55,8 +55,8 @@ |
55 | 55 |
right <- get("right", envir = pg$plot_env) |
56 | 56 |
branch.length <- get("branch.length", envir = pg$plot_env) |
57 | 57 |
ndigits <- get("ndigits", envir = pg$plot_env) |
58 |
- |
|
59 |
- |
|
58 |
+ |
|
59 |
+ |
|
60 | 60 |
pg$data <- fortify(tree, |
61 | 61 |
layout = layout, |
62 | 62 |
yscale = yscale, |
... | ... |
@@ -93,14 +93,15 @@ |
93 | 93 |
##' |
94 | 94 |
##' @rdname add_TREEINFO |
95 | 95 |
##' @title \%+>\% |
96 |
-##' @param p tree view |
|
96 |
+##' @param p tree view |
|
97 | 97 |
##' @param data data.frame |
98 | 98 |
##' @return updated data.frame |
99 | 99 |
##' @export |
100 | 100 |
##' @author Guangchuang Yu |
101 | 101 |
`%+>%` <- function(p, data) { |
102 | 102 |
df <- p$data |
103 |
- res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE) |
|
103 |
+ ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE) |
|
104 |
+ res <- merge(df, data, by.x='label', by.y=1) ## , all.x=TRUE) |
|
104 | 105 |
lv <- levels(df$panel) |
105 | 106 |
res$panel <- factor(lv[length(lv)], levels=lv) |
106 | 107 |
return(res) |