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  "Title": "Microbiome Analysis Plotting and Visualization",
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  "Description": "The miaViz package implements functions to visualize\nTreeSummarizedExperiment objects especially in the context of\nmicrobiome analysis. Part of the mia family of R/Bioconductor\npackages.",
  "biocViews": "Microbiome, Software, Visualization",
  "License": "Artistic-2.0 | file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/microbiome/miaViz",
  "BugReports": "https://github.com/microbiome/miaViz/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-02 05:56:50 UTC",
  "RemoteUrl": "https://github.com/bioc/miaViz",
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  "NeedsCompilation": "no",
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    "User": "root"
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  "Author": "Tuomas Borman [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8563-8884>),\nFelix G.M. Ernst [aut] (ORCID: <https://orcid.org/0000-0001-5064-0928>),\nLeo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>),\nBasil Courbayre [ctb],\nGiulio Benedetti [ctb] (ORCID: <https://orcid.org/0000-0002-8732-7692>),\nThéotime Pralas [ctb],\nChouaib Benchraka [ctb],\nSam Hillman [ctb],\nGeraldson Muluh [ctb],\nNoah De Gunst [ctb],\nEly Seraidarian [ctb],\nHimmi Lindgren [ctb],\nAkewak Jeba [ctb] (ORCID: <https://orcid.org/0009-0007-1347-7552>),\nVivian Ikeh [ctb]",
  "Maintainer": "Tuomas Borman <tuomas.v.borman@utu.fi>",
  "_user": "bioc",
  "_type": "src",
  "_file": "miaViz_1.21.6.tar.gz",
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  "_expires": "2027-01-10T18:00:04.000Z",
  "_created": "2026-10-02T17:46:13.000Z",
  "_published": "2026-10-02T18:00:06.959Z",
  "_bioccheck": {
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    "warning": 2,
    "note": 10
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37042305855",
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    "message": "Revert https://github.com/microbiome/miaViz/pull/233 (#234)",
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  "_homeurl": "https://github.com/microbiome/miaviz",
  "_realowner": "bioc",
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  "_exports": [
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    "colTreeData<-",
    "combineTreeData",
    "getNeatOrder",
    "plotAbundance",
    "plotAbundanceDensity",
    "plotBarplot",
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    "plotColGraph",
    "plotColTile",
    "plotColTree",
    "plotDMNFit",
    "plotFeaturePrevalence",
    "plotForest",
    "plotHeatmap",
    "plotHistogram",
    "plotJointRPCA",
    "plotLoadings",
    "plotMediation",
    "plotNMDS",
    "plotOrdination",
    "plotPrevalence",
    "plotPrevalentAbundance",
    "plotRDA",
    "plotRowGraph",
    "plotRowPrevalence",
    "plotRowTile",
    "plotRowTree",
    "plotScree",
    "plotSeries",
    "plotTaxaPrevalence",
    "rowTreeData",
    "rowTreeData<-"
  ],
  "_datasets": [
    {
      "name": "col_graph",
      "title": "miaViz example data",
      "object": "col_graph",
      "file": "col_graph.rda",
      "class": [
        "tbl_graph",
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "row_graph",
      "title": "miaViz example data",
      "object": "row_graph",
      "file": "row_graph.rda",
      "class": [
        "tbl_graph",
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "row_graph_order",
      "title": "miaViz example data",
      "object": "row_graph_order",
      "file": "row_graph_order.rda",
      "class": [
        "tbl_graph",
        "igraph"
      ],
      "fields": [],
      "table": false,
      "tojson": false
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  "_help": [
    {
      "page": "miaViz-package",
      "title": "miaViz - Microbiome Analysis Plotting and Visualization",
      "topics": [
        "miaViz-package",
        "miaViz"
      ]
    },
    {
      "page": "deprecate",
      "title": "These functions will be deprecated. Please use other functions instead.",
      "topics": [
        "deprecate",
        "plotFeaturePrevalence",
        "plotFeaturePrevalence,ANY-method",
        "plotTaxaPrevalence",
        "plotTaxaPrevalence,ANY-method"
      ]
    },
    {
      "page": "getNeatOrder",
      "title": "Sorting by radial theta angle",
      "topics": [
        "getNeatOrder",
        "getNeatOrder,matrix-method"
      ]
    },
    {
      "page": "mia-datasets",
      "title": "miaViz example data",
      "topics": [
        "col_graph",
        "mia-datasets",
        "row_graph",
        "row_graph_order"
      ]
    },
    {
      "page": "mia-plot-args",
      "title": "Additional arguments for plotting",
      "topics": [
        "mia-plot-args"
      ]
    },
    {
      "page": "plotAbundance",
      "title": "Plotting abundance data",
      "topics": [
        "plotAbundance",
        "plotAbundance,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotAbundanceDensity",
      "title": "Plot abundance density",
      "topics": [
        "plotAbundanceDensity",
        "plotAbundanceDensity,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotBoxplot",
      "title": "Create boxplot of 'assay', 'rowData' or 'colData'.",
      "topics": [
        "plotBoxplot",
        "plotBoxplot,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotCCA",
      "title": "Plot RDA or CCA object",
      "topics": [
        "plotCCA",
        "plotCCA,SingleCellExperiment-method",
        "plotRDA",
        "plotRDA,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotGraph",
      "title": "Plotting igraph objects with information from a 'SummarizedExperiment'",
      "topics": [
        "plotColGraph",
        "plotColGraph,ANY,SummarizedExperiment-method",
        "plotColGraph,SummarizedExperiment,missing-method",
        "plotGraph",
        "plotRowGraph",
        "plotRowGraph,ANY,SummarizedExperiment-method",
        "plotRowGraph,SummarizedExperiment,missing-method"
      ]
    },
    {
      "page": "plotColTile",
      "title": "Plot factor data as tiles",
      "topics": [
        "plotColTile",
        "plotColTile,SummarizedExperiment-method",
        "plotRowTile",
        "plotRowTile,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotDMN",
      "title": "Plotting Dirichlet-Multinomial Mixture Model data",
      "topics": [
        "plotDMN",
        "plotDMNFit",
        "plotDMNFit,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotForest",
      "title": "Visualize estimated results with forest plots",
      "topics": [
        "plotForest",
        "plotForest,data.frame-method",
        "plotForest,SummarizedExperiment-method",
        "plotForest,TreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "plotHeatmap",
      "title": "Visualize assay values as a heatmap",
      "topics": [
        "plotHeatmap",
        "plotHeatmap,SummarizedExperiment-method",
        "plotHeatmap,TreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "plotHistogram",
      "title": "Create histogram or barplot of 'assay', 'rowData' or 'colData'",
      "topics": [
        "plotBarplot",
        "plotBarplot,SummarizedExperiment-method",
        "plotHistogram",
        "plotHistogram,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotJointRPCA",
      "title": "Visualize Joint-RPCA results",
      "topics": [
        "plotJointRPCA",
        "plotJointRPCA,MultiAssayExperiment-method",
        "plotJointRPCA,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotLoadings",
      "title": "Plot feature loadings for TreeSummarizedExperiment objects or feature loadings numeric matrix.",
      "topics": [
        "plotLoadings",
        "plotLoadings,matrix-method",
        "plotLoadings,SingleCellExperiment-method",
        "plotLoadings,TreeSummarizedExperiment-method"
      ]
    },
    {
      "page": "plotMediation",
      "title": "Visualize mediation",
      "topics": [
        "plotMediation",
        "plotMediation,data.frame-method",
        "plotMediation,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotNMDS",
      "title": "Wrapper for scater::plotReducedDim()",
      "topics": [
        "plotNMDS"
      ]
    },
    {
      "page": "plotOrdination",
      "title": "Visualize ordination results",
      "topics": [
        "plotOrdination",
        "plotOrdination,SingleCellExperiment-method"
      ]
    },
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      "page": "plotPrevalence",
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      "headings": [
        "Installation",
        "Abundance plotting",
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        "Plotting factor data",
        "DMN fit plotting",
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