Package: miaViz 1.21.0

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_1.21.0.tar.gz
miaViz_1.21.0.zip(r-4.7)miaViz_1.21.0.zip(r-4.6)miaViz_1.21.0.zip(r-4.5)
miaViz_1.21.0.tgz(r-4.6-any)miaViz_1.21.0.tgz(r-4.5-any)
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manual.pdf |manual.html✨
card.svg |card.png
miaViz/json (API)
NEWS

# 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:

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

microbiomesoftwarevisualizationbioconductormicrobiome-analysisplotting

8.50 score 12 stars 2 packages 233 scripts 773 downloads 31 exports 160 dependencies

Last updated from:134960b88d. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR262
linux-devel-x86_64NOTE617
source / vignettesOK458
linux-release-x86_64NOTE869
macos-release-arm64NOTE416
macos-oldrel-arm64NOTE415
windows-develNOTE570
windows-releaseNOTE509
windows-oldrelNOTE383
wasm-releaseOK211

Exports:colTreeDatacolTreeData<-combineTreeDatagetNeatOrderplotAbundanceplotAbundanceDensityplotBarplotplotBoxplotplotCCAplotColGraphplotColTileplotColTreeplotDMNFitplotFeaturePrevalenceplotForestplotHistogramplotLoadingsplotMediationplotNMDSplotPrevalenceplotPrevalentAbundanceplotRDAplotRowGraphplotRowPrevalenceplotRowTileplotRowTreeplotScreeplotSeriesplotTaxaPrevalencerowTreeDatarowTreeData<-

Dependencies:abindapeaplotassortheadbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblusterbslibcachemCairocliclustercodetoolscpp11crayonDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngecodiveevaluatefarverfastmapFNNfontawesomefontBitstreamVerafontLiberationfontquiverformatRfsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesggbeeswarmggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrastrggrepelggtreegluegraphlayoutsgridExtragridGraphicsgtablehighrhtmltoolshtmlwidgetsigraphIRangesirlbaisobandjaneaustenrjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmiamimeMultiAssayExperimentnlmepatchworkpermutepheatmappillarpkgconfigplyrpngpolyclippurrrR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressreshape2rlangrmarkdownRSpectrarsvdRtsneS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscuttleSeqinfoSingleCellExperimentsitmosnowSnowballCSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystemfontstextshapingtibbletidygraphtidyrtidyselecttidytexttidytreetinytextokenizerstreeioTreeSummarizedExperimenttweenrutf8uwotvctrsveganviporviridisviridisLitewithrxfunXVectoryamlyulab.utils

miaViz

Rendered frommiaViz.Rmdusingknitr::rmarkdownon Jun 08 2026.

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

Readme and manuals

Help Manual

Help pageTopics
miaViz - Microbiome Analysis Plotting and VisualizationmiaViz-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 anglegetNeatOrder getNeatOrder,matrix-method
miaViz example datacol_graph mia-datasets row_graph row_graph_order
Additional arguments for plottingmia-plot-args
Plotting abundance dataplotAbundance plotAbundance,SummarizedExperiment-method
Plot abundance densityplotAbundanceDensity plotAbundanceDensity,SummarizedExperiment-method
Create boxplot of 'assay', 'rowData' or 'colData'.plotBoxplot plotBoxplot,SummarizedExperiment-method
Plot RDA or CCA objectplotCCA 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 tilesplotColTile plotColTile,SummarizedExperiment-method plotRowTile plotRowTile,SummarizedExperiment-method
Plotting Dirichlet-Multinomial Mixture Model dataplotDMN plotDMNFit plotDMNFit,SummarizedExperiment-method
Visualize estimated results with forest plotsplotForest 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 mediationplotMediation plotMediation,data.frame-method plotMediation,SummarizedExperiment-method
Wrapper for scater::plotReducedDim()plotNMDS
Plot prevalence informationplotPrevalence plotPrevalence,SummarizedExperiment-method plotPrevalentAbundance plotPrevalentAbundance,SummarizedExperiment-method plotRowPrevalence plotRowPrevalence,SummarizedExperiment-method
Plotting tree information enriched with informationplotColTree plotColTree,TreeSummarizedExperiment-method plotRowTree plotRowTree,TreeSummarizedExperiment-method plotTree
Create a scree plotplotScree plotScree,ANY-method plotScree,SingleCellExperiment-method
Plot SeriesplotSeries 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