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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
| Suggests Me | nullranges, rigvf |
| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/plotgardener/ |
| Package Short Url | https://bioconductor.org/packages/plotgardener/ |
| Package Downloads Report | Download Stats |