https://github.com/zachcp/phylotreewidget
HtmlWidget for phyloTree
https://github.com/zachcp/phylotreewidget
htmlwidgets phylogeny r
Last synced: 4 months ago
JSON representation
HtmlWidget for phyloTree
- Host: GitHub
- URL: https://github.com/zachcp/phylotreewidget
- Owner: zachcp
- Created: 2018-01-03T22:20:12.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-10-23T01:12:37.000Z (over 5 years ago)
- Last Synced: 2025-02-24T04:13:00.977Z (4 months ago)
- Topics: htmlwidgets, phylogeny, r
- Language: JavaScript
- Size: 1.43 MB
- Stars: 3
- Watchers: 3
- Forks: 0
- Open Issues: 7
-
Metadata Files:
- Readme: README.Rmd
- Changelog: News.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-"
)
```
# phylotree
[](https://travis-ci.org/zachcp/phyloTreeWidget)
The goal of phylotree is to provide an R interface to the phyloTree JS library in
order to make beautiful, interactive trees from any standard data source.
** NOTE: This is currently experimental and the datastructures and functions are likely to change**
## Installation
You can install phylotree from github with:
```{r gh-installation, eval = FALSE}
# install.packages("devtools")
devtools::install_github("zachcp/phyloTreeWidget")
```
## Basic Examples
This is a basic example which shows you how to generate a tree with data from
ape & phylobase.
```{r, eval=FALSE}
library(phylotree)
library(phylobase)
data(geospiza)
phylotree(tree=geospiza)
```
```{r, eval=FALSE}
library(ape)
data(bird.families)
phylotree(bird.families)
```
## Highlighting
Highlight information can be passed using the `highlight_tips` function. This uses a regex to find matches and applies a color and a size to the matching tips. These calls can be chained together to style the tip.
```{r, eval=FALSE}
# create some data
birddata <- data.frame(
node = bird.families$tip.label,
col1 = sample(1:5, length(bird.families$tip.label), replace=T),
col2 = sample(1:500, length(bird.families$tip.label), replace=T),
col4 = sample(LETTERS[1:10], length(bird.families$tip.label), replace=T)
)
# create the widget that has the data
p <- phylotree(tree=bird.families, data=birddata)
# highlight this tips by subsetting/finding that data
p %>%
highlight_tips_regex(tipregex="A", column = 'col4', highlight_color = "#8EBC66", highlight_size = 5) %>%
highlight_tips_regex(tipregex="freg", highlight_color = "#60AA9E") %>%
highlight_tips_regex(tipregex="apod", highlight_color = "#D9AD3D", highlight_size = 5)
```
## Hide Controls
You can hide the control panel to focus only on the tree.
```{r eval=FALSE}
p %>%
highlight_tips_regex(tipregex="A", column = 'col4', highlight_color = "#8EBC66", highlight_size = 5) %>%
highlight_tips_regex(tipregex="freg", highlight_color = "#60AA9E") %>%
highlight_tips_regex(tipregex="apod", highlight_color = "#D9AD3D", highlight_size = 5) %>%
hide_controls()
```
## Scale Tree Branches
```{r eval=FALSE}
p %>% scale_branchthickness()
```