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  "Title": "Fast Embedding Guided by Self-Organizing Map",
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  "Description": "Provides a smooth mapping of multidimensional points into\nlow-dimensional space defined by a self-organizing map.\nDesigned to work with 'FlowSOM' and flow-cytometry use-cases.\nSee Kratochvil et al. (2019)\n<doi:10.12688/f1000research.21642.1>.",
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  "Repository": "https://exaexa.r-universe.dev",
  "Date/Publication": "2026-03-08 21:27:35 UTC",
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    "ExprColors",
    "ExpressionGradient",
    "ExpressionPalette",
    "GQTSOM",
    "GraphCoords",
    "Initialize_PCA",
    "kMeansMap",
    "kNNCoords",
    "MapDataToCodes",
    "MSTCoords",
    "NormalizeColor",
    "PlotData",
    "PlotDefault",
    "PlotEmbed",
    "PlotGG",
    "RandomMap",
    "SOM",
    "tSNECoords",
    "UMAPCoords",
    "UMatrixCoords",
    "uwotCoords"
  ],
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    {
      "page": "ClusterPalette",
      "title": "An acceptable cluster color palette",
      "topics": [
        "ClusterPalette"
      ]
    },
    {
      "page": "EmbedSOM",
      "title": "Process the cells with SOM into a nice embedding",
      "topics": [
        "EmbedSOM"
      ]
    },
    {
      "page": "ExprColors",
      "title": "Generate colors for multi-color marker expression labeling in a single plot",
      "topics": [
        "ExprColors"
      ]
    },
    {
      "page": "ExpressionGradient",
      "title": "The ggplot2 scale gradient from ExpressionPalette.",
      "topics": [
        "ExpressionGradient"
      ]
    },
    {
      "page": "ExpressionPalette",
      "title": "Marker expression palette generator based off ColorBrewer's RdYlBu, only better for plotting of half-transparent cells",
      "topics": [
        "ExpressionPalette"
      ]
    },
    {
      "page": "GQTSOM",
      "title": "Train a Growing Quadtree Self-Organizing Map",
      "topics": [
        "GQTSOM"
      ]
    },
    {
      "page": "GraphCoords",
      "title": "Add Kamada-Kawai-generated embedding coordinates to the map",
      "topics": [
        "GraphCoords"
      ]
    },
    {
      "page": "Initialize_PCA",
      "title": "Create a grid from first 2 PCA components",
      "topics": [
        "Initialize_PCA"
      ]
    },
    {
      "page": "kMeansMap",
      "title": "Create a map from k-Means clusters",
      "topics": [
        "kMeansMap"
      ]
    },
    {
      "page": "kNNCoords",
      "title": "Add KNN-topology-based embedding coordinates to the map",
      "topics": [
        "kNNCoords"
      ]
    },
    {
      "page": "MapDataToCodes",
      "title": "Assign nearest node to each datapoint",
      "topics": [
        "MapDataToCodes"
      ]
    },
    {
      "page": "MSTCoords",
      "title": "Add MST-style embedding coordinates to the map",
      "topics": [
        "MSTCoords"
      ]
    },
    {
      "page": "NormalizeColor",
      "title": "Helper for computing colors for embedding plots",
      "topics": [
        "NormalizeColor"
      ]
    },
    {
      "page": "PlotData",
      "title": "Export a data frame for plotting with marker intensities and density.",
      "topics": [
        "PlotData"
      ]
    },
    {
      "page": "PlotDefault",
      "title": "Default plot",
      "topics": [
        "PlotDefault"
      ]
    },
    {
      "page": "PlotEmbed",
      "title": "Helper function for plotting the embedding",
      "topics": [
        "PlotEmbed"
      ]
    },
    {
      "page": "PlotGG",
      "title": "Wrap PlotData result in ggplot object.",
      "topics": [
        "PlotGG"
      ]
    },
    {
      "page": "PlotId",
      "title": "Identity on whatever",
      "topics": [
        "PlotId"
      ]
    },
    {
      "page": "RandomMap",
      "title": "Create a map by randomly selecting points",
      "topics": [
        "RandomMap"
      ]
    },
    {
      "page": "SOM",
      "title": "Build a self-organizing map",
      "topics": [
        "SOM"
      ]
    },
    {
      "page": "tSNECoords",
      "title": "Add tSNE-based coordinates to a map",
      "topics": [
        "tSNECoords"
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    {
      "page": "UMAPCoords",
      "title": "Add UMAP-based coordinates to a map",
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        "UMAPCoords"
      ]
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      "page": "UMatrixCoords",
      "title": "Add U-Matrix-optimized embedding coordinates to the map",
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        "UMatrixCoords"
      ]
    },
    {
      "page": "uwotCoords",
      "title": "Add UMAP-based coordinates to a map, using the 'uwot' package",
      "topics": [
        "uwotCoords"
      ]
    }
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  ]
}