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  "Package": "ggbrain",
  "Title": "Create Images of Volumetric Brain Data in NIfTI Format Using\n'ggplot2' Syntax",
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  "Date": "2025-11-25",
  "Authors@R": "person(\"Michael\", \"Hallquist\", , \"michael.hallquist@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5894-8038\"))",
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  "Description": "A 'ggplot2'-consistent approach to generating 2D displays\nof volumetric brain imaging data. Display data from multiple\nNIfTI images using standard 'ggplot2' conventions such scales,\nlimits, and themes to control the appearance of displays. The\nresulting plots are returned as 'patchwork' objects, inheriting\nfrom 'ggplot', allowing for any standard modifications of\ndisplay aesthetics supported by 'ggplot2'.",
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  "Repository": "https://michaelhallquist.r-universe.dev",
  "Date/Publication": "2026-06-02 20:10:24 UTC",
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    "annotate_coordinates",
    "annotate_crosshairs",
    "annotate_orientation",
    "annotate_slice",
    "cluster_slices",
    "define",
    "geom_brain",
    "geom_brain_clusterized",
    "geom_outline",
    "geom_region_label",
    "geom_region_label_repel",
    "geom_region_text",
    "geom_region_text_repel",
    "ggbrain",
    "ggbrain_images",
    "ggbrain_label",
    "ggbrain_layer",
    "ggbrain_layer_brain",
    "ggbrain_layer_outline",
    "ggbrain_panel",
    "ggbrain_plot",
    "images",
    "integer_breaks",
    "montage",
    "nn_impute",
    "range_breaks",
    "render",
    "scale_fill_bisided",
    "slices",
    "target_resolution"
  ],
  "_help": [
    {
      "page": "plus-.ggb",
      "title": "addition operator for ggb object to support ggplot-like syntax",
      "topics": [
        "+.ggb"
      ]
    },
    {
      "page": "plus-.ggbrain_images",
      "title": "summary S3 method for ggbrain_images objects addition operator for combining ggbrain_images objects",
      "topics": [
        "+.ggbrain_images"
      ]
    },
    {
      "page": "annotate_coordinates",
      "title": "Adds the coordinate labels to each panel based on the location of the slice along the slicing axis (e.g., z = 15)",
      "topics": [
        "annotate_coordinates"
      ]
    },
    {
      "page": "annotate_crosshairs",
      "title": "Annotate crosshairs at user-specified world (xyz) coordinates",
      "topics": [
        "annotate_crosshairs"
      ]
    },
    {
      "page": "annotate_orientation",
      "title": "Annotate orientation labels (L/R/A/P/S/I) on each panel using NIfTI header info",
      "topics": [
        "annotate_orientation"
      ]
    },
    {
      "page": "annotate_slice",
      "title": "Adds custom annotations to a single panel on the ggbrain plot",
      "topics": [
        "annotate_slice"
      ]
    },
    {
      "page": "cluster_slices",
      "title": "Find slice locations based on cluster centers of mass in a 3D brain image",
      "topics": [
        "cluster_slices"
      ]
    },
    {
      "page": "count_neighbors",
      "title": "This function counts the number of neighboring/touching pixels in a 2D binary image",
      "topics": [
        "count_neighbors"
      ]
    },
    {
      "page": "define",
      "title": "Adds contrast definitions to the ggbrain plot",
      "topics": [
        "define"
      ]
    },
    {
      "page": "fill_from_edge",
      "title": "This function finds holes by flood filling TRUE into a 2D binary image, starting from the edge",
      "topics": [
        "fill_from_edge"
      ]
    },
    {
      "page": "find_threads",
      "title": "This function finds 'threads' hanging off of the edges of blobs in an image, allowing the user to trim them",
      "topics": [
        "find_threads"
      ]
    },
    {
      "page": "flood_fill",
      "title": "This function flood fills a binary image with TRUE for any value of FALSE",
      "topics": [
        "flood_fill"
      ]
    },
    {
      "page": "geom_brain",
      "title": "Adds a raster layer to the ggbrain plot, displaying pixels from the specified layer definition",
      "topics": [
        "geom_brain"
      ]
    },
    {
      "page": "geom_brain_clusterized",
      "title": "Clusterize a contrast/image and display clusters as categorical fill",
      "topics": [
        "geom_brain_clusterized"
      ]
    },
    {
      "page": "geom_outline",
      "title": "Adds an outline layer to the ggbrain plot, displaying outlines from the non-missing pixels in the specified layer definition",
      "topics": [
        "geom_outline"
      ]
    },
    {
      "page": "geom_region_label",
      "title": "Variant of geom_label used for plotting region labels on slices",
      "topics": [
        "geom_region_label"
      ]
    },
    {
      "page": "geom_region_label_repel",
      "title": "Variant of geom_label_repel used for plotting region labels on slices with separation from other labels",
      "topics": [
        "geom_region_label_repel"
      ]
    },
    {
      "page": "geom_region_text",
      "title": "Variant of geom_text used for plotting region labels on slices",
      "topics": [
        "geom_region_text"
      ]
    },
    {
      "page": "geom_region_text_repel",
      "title": "Variant of geom_text_repel used for plotting region labels on slices with separation from other labels",
      "topics": [
        "geom_region_text_repel"
      ]
    },
    {
      "page": "ggbrain",
      "title": "create ggb container object for a given plot",
      "topics": [
        "ggbrain"
      ]
    },
    {
      "page": "ggbrain_images",
      "title": "R6 class for compiling images to render in ggplot",
      "topics": [
        "ggbrain_images"
      ]
    },
    {
      "page": "ggbrain_label",
      "title": "R6 class for adding labels to a ggbrain_panel",
      "topics": [
        "ggbrain_label"
      ]
    },
    {
      "page": "ggbrain_layer",
      "title": "R6 class for a single layer of a ggbrain panel",
      "topics": [
        "ggbrain_layer"
      ]
    },
    {
      "page": "ggbrain_layer_brain",
      "title": "R6 class for a single layer of a ggbrain panel using fill geom",
      "topics": [
        "ggbrain_layer_brain"
      ]
    },
    {
      "page": "ggbrain_layer_outline",
      "title": "R6 class for a single layer of a ggbrain panel using outline geom",
      "topics": [
        "ggbrain_layer_outline"
      ]
    },
    {
      "page": "ggbrain_panel",
      "title": "R6 class for a single panel of a ggbrain image",
      "topics": [
        "ggbrain_panel"
      ]
    },
    {
      "page": "ggbrain_plot",
      "title": "An R6 class for constructing a ggbrain plot from a ggbrain_slices object",
      "topics": [
        "ggbrain_plot"
      ]
    },
    {
      "page": "ggplot_add.ggbrain_label",
      "title": "S3 method to support adding ggbrain_label objects to an existing ggplot object",
      "topics": [
        "ggplot_add.ggbrain_label"
      ]
    },
    {
      "page": "ggplot_add.ggbrain_layer",
      "title": "S3 method to support adding ggbrain_layer objects to an existing ggplot object",
      "topics": [
        "ggplot_add.ggbrain_layer"
      ]
    },
    {
      "page": "ggplot_add.ggbrain_panel",
      "title": "S3 method to support adding ggbrain_layer objects to an existing ggplot object",
      "topics": [
        "ggplot_add.ggbrain_panel"
      ]
    },
    {
      "page": "images",
      "title": "Add images to a ggbrain object",
      "topics": [
        "images"
      ]
    },
    {
      "page": "integer_breaks",
      "title": "breaks function to encourage integer-valued breaks, based on input from pretty",
      "topics": [
        "integer_breaks"
      ]
    },
    {
      "page": "montage",
      "title": "Convenience function to add many slices in a montage along one of the 3D planes",
      "topics": [
        "montage"
      ]
    },
    {
      "page": "nn_impute",
      "title": "Imputes missing values in a 2D matrix based on the nearest non-missing neighbors in a given radius",
      "topics": [
        "nn_impute"
      ]
    },
    {
      "page": "plot.ggb",
      "title": "S3 method to allow for plot(x) syntax with ggbrain (ggb) objects",
      "topics": [
        "plot.ggb"
      ]
    },
    {
      "page": "plot.ggbrain_panel",
      "title": "S3 method to allow for plot() syntax with ggbrain_panel objects",
      "topics": [
        "plot.ggbrain_panel"
      ]
    },
    {
      "page": "plot.ggbrain_patchwork",
      "title": "S3 method to allow for plot() syntax with rendered ggbrain patchwork objects",
      "topics": [
        "plot.ggbrain_patchwork",
        "print.ggbrain_patchwork"
      ]
    },
    {
      "page": "plot.ggbrain_plot",
      "title": "S3 method to allow for plot() syntax with ggbrain_panel objects",
      "topics": [
        "plot.ggbrain_plot"
      ]
    },
    {
      "page": "range_breaks",
      "title": "breaks function for including min + max with labels, and a few unlabeled ticks in between",
      "topics": [
        "range_breaks"
      ]
    },
    {
      "page": "render",
      "title": "Function to convert 'ggb' object to ggplot/patchwork object",
      "topics": [
        "render"
      ]
    },
    {
      "page": "render.ggb",
      "title": "S3 method to allow for render(x) syntax with ggbrain (ggb) objects",
      "topics": [
        "render.ggb"
      ]
    },
    {
      "page": "scale_fill_bisided",
      "title": "scale for plotting separate color gradients for positive and negative values",
      "topics": [
        "scale_fill_bisided"
      ]
    },
    {
      "page": "slices",
      "title": "Adds slices to the ggbrain plot, including additional panel aesthetics",
      "topics": [
        "slices"
      ]
    },
    {
      "page": "target_resolution",
      "title": "Set the target resolution for resampling slices in a ggbrain plot",
      "topics": [
        "target_resolution"
      ]
    }
  ],
  "_readme": "https://github.com/michaelhallquist/ggbrain/raw/HEAD/README.md",
  "_rundeps": [
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  "_vignettes": [
    {
      "source": "ggbrain_aesthetics.Rmd",
      "filename": "ggbrain_aesthetics.html",
      "title": "Aesthetic refinements of ggbrain plots",
      "author": "Michael Hallquist",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Images used in this demo",
        "Adjustments to the appearance of image layers",
        "Removing small specks (remove_specks)",
        "Filling small holes (fill_holes)",
        "Trimming threads (trim_threads)",
        "Combining image cleaning operations",
        "Working with color scales",
        "Custom color scales",
        "Bisided color scales",
        "Working with categorical images and labels",
        "Mapping fills to label columns",
        "Combining fills with outlines",
        "Adding region labels",
        "Using geom_region_label_repel",
        "Adding annotations",
        "Coordinate annotations",
        "Orientation annotations",
        "Crosshair annotations",
        "Creating reusable plot components",
        "Combining ggbrain plots with patchwork",
        "Basic patchwork combinations",
        "Advanced layout with shared legend",
        "Saving ggbrain plots to file",
        "Filtering images for focused displays",
        "Target resolution for higher quality displays",
        "Other considerations",
        "Resampling images externally",
        "The hierarchy of a ggbrain plot",
        "Tips for publication-quality figures"
      ],
      "created": "2022-10-12 22:15:30",
      "modified": "2025-12-08 15:41:51",
      "commits": 7
    },
    {
      "source": "ggbrain_introduction.Rmd",
      "filename": "ggbrain_introduction.html",
      "title": "Introduction to ggbrain",
      "author": "Michael Hallquist",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Images that will be used in the demo",
        "Installing the package",
        "Building a ggbrain plot layer by layer",
        "Add images",
        "Add slices",
        "Adding slices by spatial position",
        "Adding slices by quantile",
        "Adding slices with additional aesthetic details",
        "Adding montages",
        "Automatically locating clusters and outlines",
        "Add brain overlay layers",
        "Defining an image layer",
        "Defining subset layers",
        "Defining a contrast layer",
        "Add outlines",
        "Clusterized categorical layers",
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