'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.
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ggtree extends the ggplot2 plotting system to implement the grammar of graphics for phylogenetic trees. It is designed for the visualization, manipulation, and annotation of phylogenetic trees and other tree-like structures with their associated multi-omics and clinical metadata.
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("ggtree")phylocanvas or iTOL instead because ggtree produces static vector graphics.ape::plot.phylo instead because it has zero overhead and requires no ggplot2 syntax.ggnetwork or tidygraph instead because ggtree is optimized specifically for tree topologies.phylo (from ape), treedata (from treeio), or standard R dendrograms.treeio package to import trees from diverse software formats (e.g., BEAST, MrBayes, NHX) to preserve node-level annotations.%<+% operator to seamlessly map sample traits to tree tips or internal nodes.layout = "circular" or layout = "fan" to maximize space efficiency and prevent text overlap.geom_tiplab(offset = ...) to prevent labels from clipping outside the plot boundaries.hexpand() or xlim() to extend the plot canvas.row.names or a specific ID column matches tree$tip.label.collapse() before plotting.ape: The foundational R phylogenetics package, faster for basic plotting but lacks ggplot2 integration.ggtreeExtra: An extension of ggtree designed specifically for presenting circular layouts with multiple rings of complex genomic data.phyloseq: Excellent for microbiome-specific tree plotting, but less flexible for general phylogenetic annotations than ggtree.tanggle: Specifically designed for visualizing phylogenetic networks rather than strict bifurcating trees.This skill is the knowledge layer — when, why, and how to use ggtree. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.
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概要と使いどころ
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
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This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte
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This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
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apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
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ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
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AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
日本語の概要は準備中です。原文の説明を表示しています。