miaViz
Microbiome Analysis Plotting and Visualization
Bioconductor version: 3.24 · Package version: 1.21.5
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miaViz")Details
| Maintainer | Tuomas Borman <tuomas.v.borman@utu.fi> |
| Author | Tuomas Borman [aut, cre] (ORCID: <https://orcid.org/0000-0002-8563-8884>), Felix G.M. Ernst [aut] (ORCID: <https://orcid.org/0000-0001-5064-0928>), Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>), Basil Courbayre [ctb], Giulio Benedetti [ctb] (ORCID: <https://orcid.org/0000-0002-8732-7692>), 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] (ORCID: <https://orcid.org/0009-0007-1347-7552>), Vivian Ikeh [ctb] |
| License | Artistic-2.0 | file LICENSE |
| URL | https://github.com/microbiome/miaViz |
| Bug Reports | https://github.com/microbiome/miaViz/issues |
| Downloads rank | 744 |
| Source branch | devel |
| biocViews | Microbiome, Software, Visualization |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | miaViz_1.21.5.tar.gz |
| Windows binary (x86_64) | miaViz_1.21.5.zip |
| macOS binary (arm64) | miaViz_1.21.5.tgz |
| macOS binary (x86_64) | miaViz_1.21.5.tgz |
Dependencies
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
Suggests: beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, ggpubr, knitr, maaslin3, mediation, miaTime, patchwork, rmarkdown, rstatix, shadowtext, testthat, vegan, vipor