| ... | ... |
@@ -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 |
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| 4 |
+Version: 1.7.1 |
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| 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 |
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| 2 |
+------------------------ |
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| 3 |
+ o make tree stats available in facet_plot <2016-10-24, Mon> |
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| 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 |
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| 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")
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| 36 | 36 |
##' tree <- read.tree(nwk) |
| 37 |
-##' p <- ggtree(tree) |
|
| 38 |
-##' dd <- data.frame(taxa=LETTERS[1:13], |
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| 37 |
+##' p <- ggtree(tree) |
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| 38 |
+##' dd <- data.frame(taxa=LETTERS[1:13], |
|
| 39 | 39 |
##' place=c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
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| 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$plot_env)
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| 56 | 56 |
branch.length <- get("branch.length", envir = pg$plot_env)
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| 57 | 57 |
ndigits <- get("ndigits", envir = pg$plot_env)
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| 58 |
- |
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| 59 |
- |
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| 58 |
+ |
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| 59 |
+ |
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| 60 | 60 |
pg$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 |
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| 96 |
+##' @param p tree view |
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| 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) {
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| 102 | 102 |
df <- p$data |
| 103 |
- res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
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| 103 |
+ ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
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| 104 |
+ res <- merge(df, data, by.x='label', by.y=1) ## , all.x=TRUE) |
|
| 104 | 105 |
lv <- levels(df$panel) |
| 105 | 106 |
res$panel <- factor(lv[length(lv)], levels=lv) |
| 106 | 107 |
return(res) |
