Package: miaViz 1.13.2

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]

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miaViz.pdf |miaViz.html✨
miaViz/json (API)
NEWS

# Install 'miaViz' in R:

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

Datasets:

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

On BioConductor:miaViz-1.13.0(bioc 3.20)miaViz-1.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

21 exports 2.05 score 145 dependencies

Last updated 1 months agofrom:a1378068f8

Exports:colTreeData colTreeData<-combineTreeData plotAbundance plotAbundanceDensity plotCCA plotColGraph plotColTile plotColTree plotDMNFit plotFeaturePrevalence plotPrevalence plotPrevalentAbundance plotRDA plotRowGraph plotRowTile plotRowTree plotSeries plotTaxaPrevalence rowTreeData rowTreeData<-

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

miaViz

Rendered frommiaViz.Rmdusingknitr::rmarkdownon Jun 21 2024.

Last update: 2024-04-17
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
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
Plot factor data as tiles	plotColTile plotColTile,SummarizedExperiment-method plotRowTile plotRowTile,SummarizedExperiment-method
Plotting Dirichlet-Multinomial Mixture Model data	plotDMN plotDMNFit plotDMNFit,SummarizedExperiment-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 prevalence information	plotFeaturePrevalence plotFeaturePrevalence,SummarizedExperiment-method plotPrevalence plotPrevalence,SummarizedExperiment-method plotPrevalentAbundance plotPrevalentAbundance,SummarizedExperiment-method plotTaxaPrevalence plotTaxaPrevalence,ANY-method
Plot Series	plotSeries plotSeries,SummarizedExperiment-method
Plotting tree information enriched with information	plotColTree plotColTree,TreeSummarizedExperiment-method plotRowTree plotRowTree,TreeSummarizedExperiment-method plotTree
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