plotgardener

DOI: 10.18129/B9.bioc.plotgardener  

Coordinate-Based Genomic Visualization Package for R

Bioconductor version: Release (3.17)

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

Author: Nicole Kramer [aut, cre] , Eric S. Davis [aut] , Craig Wenger [aut] , Sarah Parker [ctb], Erika Deoudes [art], Michael Love [ctb], Douglas H. Phanstiel [aut, cph]

Maintainer: Nicole Kramer <nekramer at live.unc.edu>

Installation

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

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

BiocManager::install("plotgardener")

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("plotgardener")

 

HTML	R Script	Introduction to plotgardener
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FunctionalGenomics, GenomeAnnotation, GenomeAssembly, HiC, Software, Visualization
Version	1.6.4
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	curl, data.table, dplyr, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats, strawr, tools, utils, withr
LinkingTo	Rcpp
Suggests	AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL	https://phanstiellab.github.io/plotgardener https://github.com/PhanstielLab/plotgardener
BugReports	https://github.com/PhanstielLab/plotgardener/issues
Depends On Me
Imports Me	mariner, Ularcirc
Suggests Me	nullranges
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	plotgardener_1.6.4.tar.gz
Windows Binary	plotgardener_1.6.4.zip
macOS Binary (x86_64)	plotgardener_1.6.4.tgz
macOS Binary (arm64)	plotgardener_1.6.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/plotgardener
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/plotgardener
Bioc Package Browser	https://code.bioconductor.org/browse/plotgardener/
Package Short Url	https://bioconductor.org/packages/plotgardener/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive