plotgardener

DOI: 10.18129/B9.bioc.plotgardener  

Coordinate-Based Genomic Visualization Package for R

Bioconductor version: Release (3.16)

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 (!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 1.4.2
In Bioconductor since BioC 3.14 (R-4.1) (1.5 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
LinkingTo Rcpp
Suggests AnnotationDbi, AnnotationHub, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures, GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, 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 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_1.4.2.tar.gz
Windows Binary plotgardener_1.4.2.zip
macOS Binary (x86_64) plotgardener_1.4.2.tgz
macOS Binary (arm64) plotgardener_1.4.2.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 3.16 Source Archive

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