TreeAndLeaf
This is the released version of TreeAndLeaf; for the devel version, see TreeAndLeaf.
Displaying binary trees with focus on dendrogram leaves
Bioconductor version: Release (3.23)
TreeAndLeaf implements a hybrid layout strategy that enhances leaf-level visualization in dendrograms. By integrating force-directed graph and tree layout algorithms, it enables projection of multiple layers of information onto graph–tree diagrams.
Author: Milena Cardoso [aut], Luis Rizzardi [aut], Leonardo Kume [aut], Sheyla Trefflich [ctb], Clarice Groeneveld [ctb], Mauro Castro [aut, cre]
Maintainer: Mauro Castro <mauro.a.castro at gmail.com>
citation("TreeAndLeaf")):
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("TreeAndLeaf")
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("TreeAndLeaf")| TreeAndLeaf: an graph layout to dendrograms. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, GraphAndNetwork, Network, Software, SystemsBiology, Visualization |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4) |
| Imports | RedeR(>= 3.6.1), igraph, ape |
| System Requirements | |
| URL | https://doi.org/10.1093/bioinformatics/btab819 |
| Bug Reports | https://github.com/sysbiolab/TreeAndLeaf/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr, ggtree, ggplot2, dplyr, dendextend, RColorBrewer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | RedeR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TreeAndLeaf_1.24.0.tar.gz |
| Windows Binary (x86_64) | TreeAndLeaf_1.24.0.zip |
| macOS Binary (big-sur-x86_64) | TreeAndLeaf_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | TreeAndLeaf_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TreeAndLeaf |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TreeAndLeaf |
| Bioc Package Browser | https://code.bioconductor.org/browse/TreeAndLeaf/ |
| Package Short Url | https://bioconductor.org/packages/TreeAndLeaf/ |
| Package Downloads Report | Download Stats |