Package: miaViz 1.15.2

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], 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]

miaViz_1.15.2.tar.gz
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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'))

Peer review:

Datasets:

On BioConductor:miaViz-1.15.2(bioc 3.21)miaViz-1.14.0(bioc 3.20)

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

microbiomesoftwarevisualization

6.30 score 1 packages 79 scripts 486 downloads 25 exports 192 dependencies

Last updated 1 months agofrom:94696fa7e7. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 02 2024
R-4.5-winNOTEDec 02 2024
R-4.5-linuxNOTEDec 02 2024
R-4.4-winNOTEDec 02 2024
R-4.4-macNOTEDec 02 2024
R-4.3-winNOTEDec 02 2024
R-4.3-macNOTEDec 02 2024

Exports:colTreeDatacolTreeData<-combineTreeDatagetNeatOrderplotAbundanceplotAbundanceDensityplotCCAplotColGraphplotColTileplotColTreeplotDMNFitplotFeaturePrevalenceplotLoadingsplotNMDSplotPrevalenceplotPrevalentAbundanceplotRDAplotRowGraphplotRowPrevalenceplotRowTileplotRowTreeplotSeriesplotTaxaPrevalencerowTreeDatarowTreeData<-

Dependencies:abindapeaplotaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblusterbootbslibcachemCairocheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngevaluatefansifarverfastmapFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggforceggfunggnewscaleggplot2ggplotifyggraphggrastrggrepelggtreegluegraphlayoutsgridExtragridGraphicsgtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphIRangesirlbaisobandjaneaustenrjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecyclelme4lpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmediationmemoisemgcvmiamimeminqaMultiAssayExperimentmunsellmvtnormnlmenloptrnnetopensslopenxlsxpatchworkpermutepheatmappillarpkgconfigplyrpngpolyclippurrrR.methodsS3R.ooR.utilsR6raggrappdirsrbiomRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppParallelRcppProgressreshape2rjsonrlangrmarkdownrpartRSpectrarstudioapirsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscuttleSingleCellExperimentsitmoslamsnowSnowballCSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidygraphtidyrtidyselecttidytexttidytreetinytextokenizerstreeioTreeSummarizedExperimenttweenrUCSC.utilsutf8uwotvctrsveganviporviridisviridisLitewithrxfunXVectoryamlyulab.utilszipzlibbioczoo

miaViz

Rendered frommiaViz.Rmdusingknitr::rmarkdownon Dec 02 2024.

Last update: 2024-07-09
Started: 2020-11-03

Readme and manuals

Help Manual

Help pageTopics
miaViz - Microbiome Analysis Plotting and VisualizationmiaViz-package miaViz
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
Plot RDA or CCA objectplotCCA plotCCA,matrix-method plotCCA,SingleCellExperiment-method plotRDA plotRDA,matrix-method plotRDA,SingleCellExperiment-method
Plot factor data as tilesplotColTile plotColTile,SummarizedExperiment-method plotRowTile plotRowTile,SummarizedExperiment-method
Plotting Dirichlet-Multinomial Mixture Model dataplotDMN 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 feature loadings for TreeSummarizedExperiment objects or feature loadings numeric matrix.plotLoadings plotLoadings,matrix-method plotLoadings,SingleCellExperiment-method plotLoadings,TreeSummarizedExperiment-method
Wrapper for scater::plotReducedDim()plotNMDS
Plot prevalence informationplotFeaturePrevalence plotFeaturePrevalence,ANY-method plotPrevalence plotPrevalence,SummarizedExperiment-method plotPrevalentAbundance plotPrevalentAbundance,SummarizedExperiment-method plotRowPrevalence plotRowPrevalence,SummarizedExperiment-method plotTaxaPrevalence plotTaxaPrevalence,ANY-method
Plot SeriesplotSeries plotSeries,SummarizedExperiment-method
Plotting tree information enriched with informationplotColTree 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