{
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  "Package": "miaViz",
  "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)",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/microbiome/miaViz",
  "BugReports": "https://github.com/microbiome/miaViz/issues",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make libgsl0-dev\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:29 UTC",
  "RemoteUrl": "https://github.com/bioc/miaViz",
  "RemoteRef": "HEAD",
  "RemoteSha": "134960b88df1b606079e7bfdf8d18f6f2afa0200",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-09 09:09:26 UTC",
    "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>",
  "MD5sum": "61c8b381d6304e3cfda43e43f5f23574",
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  "_created": "2026-05-09T09:09:26.000Z",
  "_published": "2026-05-22T12:58:27.041Z",
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    "source": "https://www.bioconductor.org/packages/stats/bioc/miaViz"
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.json",
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  "_homeurl": "https://github.com/microbiome/miaviz",
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  "_exports": [
    "colTreeData",
    "colTreeData<-",
    "combineTreeData",
    "getNeatOrder",
    "plotAbundance",
    "plotAbundanceDensity",
    "plotBarplot",
    "plotBoxplot",
    "plotCCA",
    "plotColGraph",
    "plotColTile",
    "plotColTree",
    "plotDMNFit",
    "plotFeaturePrevalence",
    "plotForest",
    "plotHistogram",
    "plotLoadings",
    "plotMediation",
    "plotNMDS",
    "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
    }
  ],
  "_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,matrix-method",
        "plotCCA,SingleCellExperiment-method",
        "plotRDA",
        "plotRDA,matrix-method",
        "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": "plotHistogram",
      "title": "Create histogram or barplot of 'assay', 'rowData' or 'colData'",
      "topics": [
        "plotBarplot",
        "plotBarplot,SummarizedExperiment-method",
        "plotHistogram",
        "plotHistogram,SummarizedExperiment-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": "plotPrevalence",
      "title": "Plot prevalence information",
      "topics": [
        "plotPrevalence",
        "plotPrevalence,SummarizedExperiment-method",
        "plotPrevalentAbundance",
        "plotPrevalentAbundance,SummarizedExperiment-method",
        "plotRowPrevalence",
        "plotRowPrevalence,SummarizedExperiment-method"
      ]
    },
    {
      "page": "plotTree",
      "title": "Plotting tree information enriched with information",
      "topics": [
        "plotColTree",
        "plotColTree,TreeSummarizedExperiment-method",
        "plotRowTree",
        "plotRowTree,TreeSummarizedExperiment-method",
        "plotTree"
      ]
    },
    {
      "page": "plotScree",
      "title": "Create a scree plot",
      "topics": [
        "plotScree",
        "plotScree,ANY-method",
        "plotScree,SingleCellExperiment-method"
      ]
    },
    {
      "page": "plotSeries",
      "title": "Plot Series",
      "topics": [
        "plotSeries",
        "plotSeries,SummarizedExperiment-method"
      ]
    },
    {
      "page": "treeData",
      "title": "Adding information to tree data in 'TreeSummarizedExperiment'",
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