Package: miaViz 1.15.6

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], Nitesh Turaga [ctb], Chouaib Benchraka [ctb], Sam Hillman [ctb], Muluh Muluh [ctb], Noah De Gunst [ctb], Ely Seraidarian [ctb], Himmi Lindgren [ctb], Vivian Ikeh [ctb]

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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:

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

On BioConductor:miaViz-1.15.5(bioc 3.21)miaViz-1.14.0(bioc 3.20)

microbiome software visualization bioconductor microbiome-analysis plotting

8.59 score 10 stars 1 packages 81 scripts 554 downloads 27 exports 175 dependencies

Last updated 20 days agofrom:9e98d3b3db. Checks:1 OK, 5 NOTE, 1 FAILURE, 1 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 31 2025
R-4.5-win	NOTE	Jan 31 2025
R-4.5-mac	WARNING	Jan 31 2025
R-4.5-linux	NOTE	Jan 31 2025
R-4.4-win	NOTE	Jan 31 2025
R-4.4-mac	NOTE	Jan 31 2025
R-4.3-win	NOTE	Jan 31 2025
R-4.3-mac	OUTDATED	Jan 01 2025

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

Dependencies:abind ape aplot askpass assorthead beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bluster cachem Cairo cellranger cli clipr cluster codetools colorspace commonmark cpp11 crayon curl DBI DECIPHER decontam DelayedArray DelayedMatrixStats digest DirichletMultinomial dplyr dqrng emmeans estimability fansi farver fastmap fillpattern FNN formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrastr ggrepel ggtext ggtree glue graphlayouts gridExtra gridGraphics gridtext gtable hms httr igraph IRanges irlba isoband janeaustenr jpeg jsonlite labeling lambda.r lattice lazyeval lifecycle magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mia mime MultiAssayExperiment munsell mvtnorm nlme numDeriv openssl parallelly patchwork permute pheatmap pillar pkgconfig plyr png polyclip prettyunits progress purrr R6 ragg rbiom RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress readr readxl rematch reshape2 rlang RSpectra rsvd Rtsne S4Arrays S4Vectors ScaledMatrix scales scater scuttle SingleCellExperiment sitmo slam snow SnowballC SparseArray sparseMatrixStats stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidygraph tidyr tidyselect tidytext tidytree tokenizers treeio TreeSummarizedExperiment tweenr tzdb UCSC.utils utf8 uwot vctrs vegan vipor viridis viridisLite vroom withr xfun xml2 XVector yulab.utils

miaViz

Rendered frommiaViz.Rmdusingknitr::rmarkdownon Jan 31 2025.

Last update: 2025-01-15
Started: 2020-11-03

Citation

Development and contributors

Readme and manuals

Help Manual

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
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
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