Package: miaViz 1.21.1

Tuomas Borman

miaViz: Microbiome Analysis Plotting and Visualization

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.

Authors: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]

miaViz_1.21.1.tar.gz
miaViz_1.21.1.zip(r-4.7)miaViz_1.21.1.zip(r-4.6)miaViz_1.21.1.zip(r-4.5)
miaViz_1.21.1.tgz(r-4.6-any)miaViz_1.21.1.tgz(r-4.5-any)
miaViz_1.21.1.tar.gz(r-4.7-any)miaViz_1.21.1.tar.gz(r-4.6-any)
miaViz_1.21.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
miaViz/json (API)

# Install 'miaViz' in R:

install.packages('miaViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/microbiome/miaviz/issues

Datasets:

col_graph - MiaViz example data
row_graph - MiaViz example data
row_graph_order - MiaViz example data

On BioConductor:miaViz-1.21.0(bioc 3.24)miaViz-1.20.0(bioc 3.23)

microbiome software visualization bioconductor microbiome-analysis plotting

9.24 score 12 stars 2 packages 234 scripts 773 downloads 31 exports 160 dependencies

Last updated from:4484aaddce. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	242
linux-devel-x86_64	NOTE	591
source / vignettes	OK	386
linux-release-x86_64	NOTE	596
macos-release-arm64	NOTE	370
macos-oldrel-arm64	NOTE	352
windows-devel	NOTE	548
windows-release	NOTE	554
windows-oldrel	NOTE	508
wasm-release	OK	204

Exports:colTreeData colTreeData<-combineTreeData getNeatOrder plotAbundance plotAbundanceDensity plotBarplot plotBoxplot plotCCA plotColGraph plotColTile plotColTree plotDMNFit plotFeaturePrevalence plotForest plotHistogram plotLoadings plotMediation plotNMDS plotPrevalence plotPrevalentAbundance plotRDA plotRowGraph plotRowPrevalence plotRowTile plotRowTree plotScree plotSeries plotTaxaPrevalence rowTreeData rowTreeData<-

Dependencies:abind ape aplot assorthead base64enc beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bluster bslib cachem Cairo cli cluster codetools cpp11 crayon DBI DECIPHER decontam DelayedArray DelayedMatrixStats digest DirichletMultinomial dplyr dqrng ecodive evaluate farver fastmap FNN fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics GenomicRanges ggbeeswarm ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrastr ggrepel ggtree glue graphlayouts gridExtra gridGraphics gtable highr htmltools htmlwidgets igraph IRanges irlba isoband janeaustenr jquerylib jsonlite knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mia mime MultiAssayExperiment nlme patchwork permute pheatmap pillar pkgconfig plyr png polyclip purrr R6 ragg rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress reshape2 rlang rmarkdown RSpectra rsvd Rtsne S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scuttle Seqinfo SingleCellExperiment sitmo snow SnowballC SparseArray sparseMatrixStats stringi stringr SummarizedExperiment systemfonts textshaping tibble tidygraph tidyr tidyselect tidytext tidytree tinytex tokenizers treeio TreeSummarizedExperiment tweenr utf8 uwot vctrs vegan vipor viridis viridisLite withr xfun XVector yaml yulab.utils

miaViz

Rendered frommiaViz.Rmdusingknitr::rmarkdown

Last update: 2025-10-14
Started: 2020-11-03

Help page	Topics
miaViz - Microbiome Analysis Plotting and Visualization	miaViz-package miaViz
These functions will be deprecated. Please use other functions instead.	deprecate plotFeaturePrevalence plotFeaturePrevalence,ANY-method plotTaxaPrevalence plotTaxaPrevalence,ANY-method
Sorting by radial theta angle	getNeatOrder getNeatOrder,matrix-method
miaViz example data	col_graph mia-datasets row_graph row_graph_order
Additional arguments for plotting	mia-plot-args
Plotting abundance data	plotAbundance plotAbundance,SummarizedExperiment-method
Plot abundance density	plotAbundanceDensity plotAbundanceDensity,SummarizedExperiment-method
Create boxplot of 'assay', 'rowData' or 'colData'.	plotBoxplot plotBoxplot,SummarizedExperiment-method
Plot RDA or CCA object	plotCCA plotCCA,matrix-method plotCCA,SingleCellExperiment-method plotRDA plotRDA,matrix-method plotRDA,SingleCellExperiment-method
Plotting igraph objects with information from a 'SummarizedExperiment'	plotColGraph plotColGraph,ANY,SummarizedExperiment-method plotColGraph,SummarizedExperiment,missing-method plotGraph plotRowGraph plotRowGraph,ANY,SummarizedExperiment-method plotRowGraph,SummarizedExperiment,missing-method
Plot factor data as tiles	plotColTile plotColTile,SummarizedExperiment-method plotRowTile plotRowTile,SummarizedExperiment-method
Plotting Dirichlet-Multinomial Mixture Model data	plotDMN plotDMNFit plotDMNFit,SummarizedExperiment-method
Visualize estimated results with forest plots	plotForest plotForest,data.frame-method plotForest,SummarizedExperiment-method plotForest,TreeSummarizedExperiment-method
Create histogram or barplot of 'assay', 'rowData' or 'colData'	plotBarplot plotBarplot,SummarizedExperiment-method plotHistogram plotHistogram,SummarizedExperiment-method
Plot feature loadings for TreeSummarizedExperiment objects or feature loadings numeric matrix.	plotLoadings plotLoadings,matrix-method plotLoadings,SingleCellExperiment-method plotLoadings,TreeSummarizedExperiment-method
Visualize mediation	plotMediation plotMediation,data.frame-method plotMediation,SummarizedExperiment-method
Wrapper for scater::plotReducedDim()	plotNMDS
Plot prevalence information	plotPrevalence plotPrevalence,SummarizedExperiment-method plotPrevalentAbundance plotPrevalentAbundance,SummarizedExperiment-method plotRowPrevalence plotRowPrevalence,SummarizedExperiment-method
Plotting tree information enriched with information	plotColTree plotColTree,TreeSummarizedExperiment-method plotRowTree plotRowTree,TreeSummarizedExperiment-method plotTree
Create a scree plot	plotScree plotScree,ANY-method plotScree,SingleCellExperiment-method
Plot Series	plotSeries plotSeries,SummarizedExperiment-method
Adding information to tree data in 'TreeSummarizedExperiment'	colTreeData colTreeData,TreeSummarizedExperiment-method colTreeData<- colTreeData<-,TreeSummarizedExperiment-method combineTreeData combineTreeData,phylo-method combineTreeData,treedata-method rowTreeData rowTreeData,TreeSummarizedExperiment-method rowTreeData<- rowTreeData<-,TreeSummarizedExperiment-method treeData

Package: miaViz 1.21.1

miaViz: Microbiome Analysis Plotting and Visualization

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