miaViz
This is the development version of miaViz; for the stable release version, see miaViz.
Microbiome Analysis Plotting and Visualization
Bioconductor version: Development (3.24)
The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.
Author: Tuomas Borman [aut, cre]
, Felix G.M. Ernst [aut]
, Leo Lahti [aut]
, Basil Courbayre [ctb], Giulio Benedetti [ctb]
, Théotime Pralas [ctb], Chouaib Benchraka [ctb], Sam Hillman [ctb], Geraldson Muluh [ctb], Noah De Gunst [ctb], Ely Seraidarian [ctb], Himmi Lindgren [ctb], Akewak Jeba [ctb]
, Vivian Ikeh [ctb]
Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>
citation("miaViz")):
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("miaViz")
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("miaViz")| miaViz | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Microbiome, Software, Visualization |
| Version | 1.21.3 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | Artistic-2.0 | file LICENSE |
| Depends | R (>= 4.1), ggplot2, ggraph (>= 2.0), mia(>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment |
| Imports | ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggtree, grid, methods, patchwork, rlang, S4Vectors, scales, scater, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis |
| System Requirements | |
| URL | https://github.com/microbiome/miaViz |
| Bug Reports | https://github.com/microbiome/miaViz/issues |
See More
| Suggests | beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, ggpubr, knitr, maaslin3, mediation, miaTime, patchwork, rmarkdown, rstatix, shadowtext, testthat, vegan, vipor |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | iSEEtree |
| Suggests Me | HoloFoodR, MGnifyR, mia, miaSim, miaTime, OMA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | miaViz_1.21.3.tar.gz |
| Windows Binary (x86_64) | miaViz_1.21.1.zip |
| macOS Binary (big-sur-x86_64) | miaViz_1.21.3.tgz |
| macOS Binary (sonoma-arm64) | miaViz_1.21.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/miaViz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/miaViz |
| Bioc Package Browser | https://code.bioconductor.org/browse/miaViz/ |
| Package Short Url | https://bioconductor.org/packages/miaViz/ |
| Package Downloads Report | Download Stats |