plotgardener

DOI: 10.18129/B9.bioc.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 (3.15)

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>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews FunctionalGenomics, GenomeAnnotation, GenomeAssembly, HiC, Software, Visualization
Version 1.1.2
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.1.0)
Imports curl, data.table, dplyr, grDevices, grid, ggplotify, methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats, strawr, tools, utils
LinkingTo Rcpp
Suggests AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, IRanges, knitr, org.Hs.eg.db, rtracklayer, plotgardenerData, 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
Suggests Me nullranges
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/plotgardener
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/plotgardener
Package Short Url https://bioconductor.org/packages/plotgardener/
Package Downloads Report Download Stats

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