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 (3.24)
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("plotgardener")):Nicole Kramer, Eric S. Davis, Craig Wenger, Douglas H. Phanstiel. plotgardener: Coordinate-Based Genomic Visualization Package for R. doi:10.18129/B9.bioc.plotgardener, R package version 1.19.0, https://bioconductor.org/packages/plotgardener.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | FunctionalGenomics, GenomeAnnotation, GenomeAssembly, HiC, Software, Visualization |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2.0) |
| 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, TxDb.Hsapiens.UCSC.hg38.knownGene |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | DegCre, mariner, Ularcirc |
| Suggests Me | nullranges, rigvf |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | plotgardener_1.19.0.tar.gz |
| Windows Binary (x86_64) | plotgardener_1.19.0.zip |
| macOS Binary (big-sur-x86_64) | plotgardener_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | plotgardener_1.19.0.tgz |
| 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 |