plotgardener

This is the released version of plotgardener; for the devel version, see plotgardener.

Coordinate-Based Genomic Visualization Package for R

Bioconductor version: Release (3.20)

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, cre, cph]

Maintainer: Nicole Kramer <nekramer27 at gmail.com>, Douglas Phanstiel <douglas_phanstiel at med.unc.edu>

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

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	FunctionalGenomics, GenomeAnnotation, GenomeAssembly, HiC, Software, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 years)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue, grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr, Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils, withr
System Requirements
URL	https://phanstiellab.github.io/plotgardener https://github.com/PhanstielLab/plotgardener
Bug Reports	https://github.com/PhanstielLab/plotgardener/issues

Suggests	AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, pdftools, png, rmarkdown, scales, showtext, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene
Linking To	Rcpp
Enhances
Depends On Me
Imports Me	DegCre, Ularcirc, mariner
Suggests Me	nullranges
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	plotgardener_1.12.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	plotgardener_1.12.0.tgz
macOS Binary (arm64)	plotgardener_1.12.0.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