plotgardener

This is the development version of plotgardener; for the stable release version, see plotgardener.

Coordinate-Based Genomic Visualization Package for R


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews FunctionalGenomics, GenomeAnnotation, GenomeAssembly, HiC, Software, Visualization
Version 1.11.3
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
See More
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, mariner, Ularcirc
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_1.11.3.tar.gz
Windows Binary plotgardener_1.11.0.zip
macOS Binary (x86_64) plotgardener_1.11.3.tgz
macOS Binary (arm64) plotgardener_1.11.3.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