{"id":20046485,"url":"https://github.com/zachcp/phylotreewidget","last_synced_at":"2026-04-18T14:04:45.432Z","repository":{"id":146169902,"uuid":"116187708","full_name":"zachcp/phyloTreeWidget","owner":"zachcp","description":"HtmlWidget for phyloTree","archived":false,"fork":false,"pushed_at":"2019-10-23T01:12:37.000Z","size":1499,"stargazers_count":3,"open_issues_count":7,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2026-03-29T17:25:15.944Z","etag":null,"topics":["htmlwidgets","phylogeny","r"],"latest_commit_sha":null,"homepage":null,"language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/zachcp.png","metadata":{"files":{"readme":"README.Rmd","changelog":"News.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-01-03T22:20:12.000Z","updated_at":"2021-02-05T08:36:35.000Z","dependencies_parsed_at":"2023-09-16T11:25:38.721Z","dependency_job_id":null,"html_url":"https://github.com/zachcp/phyloTreeWidget","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/zachcp/phyloTreeWidget","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2FphyloTreeWidget","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2FphyloTreeWidget/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2FphyloTreeWidget/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2FphyloTreeWidget/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/zachcp","download_url":"https://codeload.github.com/zachcp/phyloTreeWidget/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/zachcp%2FphyloTreeWidget/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31971500,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-18T00:39:45.007Z","status":"online","status_checked_at":"2026-04-18T02:00:07.018Z","response_time":103,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["htmlwidgets","phylogeny","r"],"created_at":"2024-11-13T11:24:13.474Z","updated_at":"2026-04-18T14:04:41.869Z","avatar_url":"https://github.com/zachcp.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r setup, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\"\n)\n```\n# phylotree\n\n[![Build Status](https://travis-ci.org/zachcp/phyloTreeWidget.svg?branch=master)](https://travis-ci.org/zachcp/phyloTreeWidget)\n\nThe goal of phylotree is to provide an R interface to the phyloTree JS library in \norder to make beautiful, interactive trees from any standard data source.\n\n** NOTE: This is currently experimental and the datastructures and functions are likely to change**\n\n## Installation\n\nYou can install phylotree from github with:\n\n```{r gh-installation, eval = FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"zachcp/phyloTreeWidget\")\n\n```\n\n## Basic Examples\n\nThis is a basic example which shows you how to generate a tree with data from \nape \u0026 phylobase.\n\n```{r, eval=FALSE}\nlibrary(phylotree)\nlibrary(phylobase)\ndata(geospiza)\nphylotree(tree=geospiza)\n\n```\n\n![](geospiza.png)\n\n\n\n```{r, eval=FALSE}\nlibrary(ape)\ndata(bird.families)\nphylotree(bird.families)\n```\n![](phylotree1.png)\n\n## Highlighting\n\nHighlight information can be passed using the `highlight_tips` function. This uses a regex to find matches and applies a color and a size to the matching tips. These calls can be chained together to style the tip.\n\n\n```{r, eval=FALSE}\n\n# create some data\nbirddata \u003c- data.frame(\n  node = bird.families$tip.label,\n  col1 = sample(1:5, length(bird.families$tip.label), replace=T),\n  col2 = sample(1:500, length(bird.families$tip.label), replace=T),\n  col4 = sample(LETTERS[1:10], length(bird.families$tip.label), replace=T)\n)\n\n# create the widget that has the data\np \u003c- phylotree(tree=bird.families, data=birddata)\n\n# highlight this tips by subsetting/finding that data\np %\u003e% \n  highlight_tips_regex(tipregex=\"A\", column = 'col4', highlight_color = \"#8EBC66\", highlight_size = 5) %\u003e%\n  highlight_tips_regex(tipregex=\"freg\", highlight_color = \"#60AA9E\") %\u003e%\n  highlight_tips_regex(tipregex=\"apod\", highlight_color = \"#D9AD3D\", highlight_size = 5)\n\n```\n![](phylotree_highlight.png)\n## Hide Controls\n\nYou can hide the control panel to focus only on the tree.\n\n```{r eval=FALSE}\np %\u003e% \n  highlight_tips_regex(tipregex=\"A\", column = 'col4', highlight_color = \"#8EBC66\", highlight_size = 5) %\u003e%\n  highlight_tips_regex(tipregex=\"freg\", highlight_color = \"#60AA9E\") %\u003e%\n  highlight_tips_regex(tipregex=\"apod\", highlight_color = \"#D9AD3D\", highlight_size = 5) %\u003e%\n  hide_controls()\n```\n\n## Scale Tree Branches\n\n```{r eval=FALSE}\np %\u003e% scale_branchthickness()\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzachcp%2Fphylotreewidget","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzachcp%2Fphylotreewidget","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzachcp%2Fphylotreewidget/lists"}