ggtreeDendro
This is the released version of ggtreeDendro; for the devel version, see ggtreeDendro.
Drawing 'dendrogram' using 'ggtree'
Bioconductor version: Release (3.23)
Offers a set of 'autoplot' methods to visualize tree-like structures (e.g., hierarchical clustering and classification/regression trees) using 'ggtree'. You can adjust graphical parameters using grammar of graphic syntax and integrate external data to the tree.
Author: Guangchuang Yu [aut, cre, cph]
, Shuangbin Xu [ctb]
, Chuanjie Zhang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("ggtreeDendro")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggtreeDendro")
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("ggtreeDendro")| Visualizing Dendrogram using ggtree | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, DecisionTree, Phylogenetics, Software, Visualization |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | Artistic-2.0 |
| Depends | ggtree(>= 3.5.3) |
| Imports | ggplot2, stats, tidytree, utils |
| System Requirements | |
| URL |
See More
| Suggests | aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust, rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils |
| 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 | ggtreeDendro_1.14.0.tar.gz |
| Windows Binary (x86_64) | ggtreeDendro_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | ggtreeDendro_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | ggtreeDendro_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ggtreeDendro |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ggtreeDendro |
| Bioc Package Browser | https://code.bioconductor.org/browse/ggtreeDendro/ |
| Package Short Url | https://bioconductor.org/packages/ggtreeDendro/ |
| Package Downloads Report | Download Stats |