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ggkegg

KEGG pathway visualization by ggplot2


Bioconductor version: Release (3.18)

This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.

Author: Noriaki Sato [cre, aut]

Maintainer: Noriaki Sato <nori at hgc.jp>

Citation (from within R, enter citation("ggkegg")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggkegg")

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("ggkegg")
ggkegg HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, KEGG, Pathways, Software
Version 1.0.13
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph
Imports BiocFileCache, GetoptLong, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, org.Hs.eg.db, methods, utils, stats, AnnotationDbi, grDevices, gtable
System Requirements
URL https://github.com/noriakis/ggkegg
Bug Reports https://github.com/noriakis/ggkegg/issues
See More
Suggests knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0)
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 ggkegg_1.0.13.tar.gz
Windows Binary ggkegg_1.0.13.zip
macOS Binary (x86_64) ggkegg_1.0.13.tgz
macOS Binary (arm64) ggkegg_1.0.13.tgz
Source Repository git clone https://git.bioconductor.org/packages/ggkegg
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggkegg
Bioc Package Browser https://code.bioconductor.org/browse/ggkegg/
Package Short Url https://bioconductor.org/packages/ggkegg/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive