phylobar
This is the development version of phylobar; to use it, please install the devel version of Bioconductor.
Interactive construction of stacked barplots using hierarchies
Bioconductor version: Development (3.24)
The phylobar package supports interactive visualization of microbiome data by allowing a stacked barplot to be constructed using a guiding taxonomic or phylogenetic hierarchy. The package provides a strategy for collapsing and expanding the hierarchy to different levels of resolution and then for interactively "painting" the stacked barplot by placing the mouse over different subtrees. This makes it possible to interactively test different color palettes at different resolution and identify taxonomic groups with interesting variation before settling on a final stacked barplot. One advantage of the approach is that multiple levels of taxonomic resolution can be compared at once within the same view.
Author: Kris Sankaran [aut, cre, fnd]
, Megan Kuo [aut], Saritha Kodikara [aut], Jiadong Mao [aut]
Maintainer: Kris Sankaran <ksankaran at wisc.edu>
citation("phylobar")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("phylobar")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("phylobar")| 1. Getting Started | HTML | R Script |
| 2. Building Trees from Taxonomies | HTML | R Script |
| 3. Customizing Style in phylobar | HTML | R Script |
| 4. Exporting to Vector Graphics Format | HTML | R Script |
| 5. Working with phyloseq and TreeSummarizedExperiment versions of the Global Patterns Dataset | HTML | R Script |
| 6. Tipping Points in the Atlas 1006 Dataset | HTML | R Script |
| 7. Differences in the Community Composition due to Diet | HTML | R Script |
| 8. The Effect of a High-Fat High-Sugar (HFHS) Diet on the Mouse Microbiome | HTML | R Script |
| 9. Cell-type Hierarchy Informs COVID-19 Immunology | HTML | R Script |
| Reference Manual |
Details
| biocViews | Microbiome, Phylogenetics, Software, Visualization |
| Version | 0.99.12 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.6.0) |
| Imports | ape, cluster, htmlwidgets, knitr, phangorn, purrr |
| System Requirements | |
| URL | https://github.com/mkdiro-O/phylobar http://mkdiro-o.github.io/phylobar |
| Bug Reports | https://github.com/mkdiro-O/phylobar/issues |
See More
| Suggests | BiocStyle, DESeq2, dplyr, ggplot2, mia, miaViz, microbiome, phyloseq, readr, rmarkdown, scater, seriation, stringr, testthat (>= 3.0.0), tibble, tidyr, zen4R |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | phylobar_0.99.12.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/phylobar |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/phylobar |
| Bioc Package Browser | https://code.bioconductor.org/browse/phylobar/ |
| Package Short Url | https://bioconductor.org/packages/phylobar/ |
| Package Downloads Report | Download Stats |