{
  "_id": "6a17effcacfb0bcc41da6832",
  "Package": "ggcyto",
  "Type": "Package",
  "Title": "Visualize Cytometry data with ggplot",
  "Version": "1.41.1",
  "Date": "2015-11-02",
  "Author": "Mike Jiang",
  "Maintainer": "Mike Jiang <mike@ozette.com>",
  "Description": "With the dedicated fortify method implemented for flowSet,\nncdfFlowSet and GatingSet classes, both raw and gated flow\ncytometry data can be plotted directly with ggplot. ggcyto\nwrapper and some customed layers also make it easy to add gates\nand population statistics to the plot.",
  "VignetteBuilder": "knitr",
  "License": "file LICENSE",
  "URL": "https://github.com/RGLab/ggcyto/issues",
  "biocViews": "ImmunoOncology, FlowCytometry, CellBasedAssays,\nInfrastructure, Visualization",
  "Collate": "'AllClasses.R' 'autoplot.R' 'axis_inverse_trans.R'\n'compute_stats.R' 'faust_gating_plot.R' 'fortify.R'\n'fortify_fs.R' 'geom_gate.R' 'geom_hvline.R'\n'geom_multi_range.R' 'geom_overlay.R' 'geom_stats.R'\n'getFlowFrame.R' 'ggcyto.R' 'ggcyto_GatingLayout.R'\n'ggcyto_GatingSet.R' 'ggcyto_flowSet.R' 'labs.R' 'ggcyto_par.R'\n'ggplot_data_frame.R' 'merge.quad.gates.R' 'replace_data.R'\n'scales_flowCore_fasinh.R' 'scales_flowJo_biexp.R'\n'scales_flowJo_fasinh.R' 'scales_logicle.R' 'stat_position.R'\n'transform_gate.R' 'utility.R'",
  "RoxygenNote": "7.2.1",
  "Roxygen": "list(markdown=TRUE)",
  "Config/pak/sysreqs": "libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-27 20:51:51 UTC",
  "RemoteUrl": "https://github.com/bioc/ggcyto",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "_created": "2026-05-28T06:56:16.000Z",
  "_published": "2026-05-28T07:34:20.701Z",
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  "_exports": [
    ".fr2dt",
    ".fs2dt",
    "%+%",
    "as.ggplot",
    "autoplot",
    "axis_x_inverse_trans",
    "axis_y_inverse_trans",
    "compute_stats",
    "faust_gating_plot",
    "flowCore_asinht_trans",
    "fortify_fs",
    "gate_null",
    "geom_gate",
    "geom_hvline",
    "geom_multi_range",
    "geom_overlay",
    "geom_stats",
    "getFlowFrame",
    "ggcyto",
    "ggcyto_arrange",
    "ggcyto_par_default",
    "ggcyto_par_set",
    "is.ggcyto",
    "is.ggcyto_flowSet",
    "is.ggcyto_par",
    "labs_cyto",
    "marginalFilter",
    "print",
    "rescale_gate",
    "scale_x_flowCore_fasinh",
    "scale_x_flowjo_biexp",
    "scale_x_flowJo_biexp",
    "scale_x_flowjo_fasinh",
    "scale_x_flowJo_fasinh",
    "scale_x_logicle",
    "scale_y_flowCore_fasinh",
    "scale_y_flowjo_biexp",
    "scale_y_flowJo_biexp",
    "scale_y_flowjo_fasinh",
    "scale_y_flowJo_fasinh",
    "scale_y_logicle",
    "show",
    "stat_position",
    "stats_null",
    "transform"
  ],
  "_help": [
    {
      "page": "as.ggplot",
      "title": "It fortifies the data, fills some default settings and returns a regular ggplot object.",
      "topics": [
        "as.ggplot"
      ]
    },
    {
      "page": "autoplot",
      "title": "Plot cytometry data in one or two dimension with the ggcyto package.",
      "topics": [
        "autoplot",
        "autoplot.cytoframe",
        "autoplot.cytoset",
        "autoplot.flowFrame",
        "autoplot.flowSet",
        "autoplot.GatingHierarchy",
        "autoplot.GatingSet",
        "autoplot.GatingSetList",
        "autoplot.ncdfFlowList"
      ]
    },
    {
      "page": "axis_x_inverse_trans",
      "title": "Display ggcyto axis labels using their raw values (as stored in the data structure)",
      "topics": [
        "axis_x_inverse_trans",
        "axis_y_inverse_trans"
      ]
    },
    {
      "page": "compute_stats",
      "title": "compute the statistics of the cell population defined by gates",
      "topics": [
        "compute_stats"
      ]
    },
    {
      "page": "faust_gating_plot",
      "title": "plot faust gating schemes",
      "topics": [
        "faust_gating_plot"
      ]
    },
    {
      "page": "flowCore_asinht_trans",
      "title": "Inverse hyperbolic sine transformation(flowCore version).",
      "topics": [
        "flowCore_asinht_trans"
      ]
    },
    {
      "page": "fortify_fs",
      "title": "Fortify a model into flowSet object",
      "topics": [
        "fortify_fs",
        "fortify_fs.cytoframe",
        "fortify_fs.default",
        "fortify_fs.flowFrame",
        "fortify_fs.flowSet",
        "fortify_fs.GatingSet",
        "fortify_fs.GatingSetList"
      ]
    },
    {
      "page": "fortify.flowSet",
      "title": "Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table",
      "topics": [
        "fortify",
        "fortify.cytoframe",
        "fortify.cytoset",
        "fortify.flowFrame",
        "fortify.flowSet",
        "fortify.GatingSet",
        "fortify.GatingSetList",
        "fortify.ncdfFlowList"
      ]
    },
    {
      "page": "fortify.ellipsoidGate",
      "title": "Convert a ellipsoidGate to a data.table useful for ggplot",
      "topics": [
        "fortify.ellipsoidGate"
      ]
    },
    {
      "page": "fortify.filterList",
      "title": "Convert a filterList to a data.table useful for ggplot",
      "topics": [
        "fortify.filterList"
      ]
    },
    {
      "page": "fortify.multiRangeGate",
      "title": "Convert a multiRangeGate to a data.table useful for ggplot",
      "topics": [
        "fortify.multiRangeGate"
      ]
    },
    {
      "page": "fortify.polygonGate",
      "title": "Convert a polygonGate to a data.table useful for ggplot",
      "topics": [
        "fortify.polygonGate"
      ]
    },
    {
      "page": "fortify.rectangleGate",
      "title": "Convert a rectangleGate to a data.table useful for ggplot",
      "topics": [
        "fortify.rectangleGate"
      ]
    },
    {
      "page": "gate_null",
      "title": "clear all the geom_gate() layer previously added",
      "topics": [
        "gate_null"
      ]
    },
    {
      "page": "geom_gate",
      "title": "Add a gate layer to a ggcyto plot.",
      "topics": [
        "geom_gate",
        "geom_gate.character",
        "geom_gate.default",
        "geom_gate.filter",
        "geom_gate.filterList",
        "geom_gate.filters",
        "geom_gate.filtersList",
        "geom_gate.list",
        "geom_gate.logical",
        "geom_gate.logicalFilterResult",
        "geom_gate.quadGate"
      ]
    },
    {
      "page": "geom_hvline",
      "title": "Vertical or horizontal line.",
      "topics": [
        "geom_hvline"
      ]
    },
    {
      "page": "geom_multi_range",
      "title": "Draw multi-ranges as multiple rectangles on 1D or 2D plot",
      "topics": [
        "geom_multi_range"
      ]
    },
    {
      "page": "geom_overlay",
      "title": "Overlay a population on an existing ggcyto plot analogous to backgating.",
      "topics": [
        "geom_overlay",
        "geom_overlay.character",
        "geom_overlay.default",
        "geom_overlay.flowFrame",
        "geom_overlay.flowSet",
        "geom_overlay.ncdfFlowList"
      ]
    },
    {
      "page": "geom_stats",
      "title": "Add a popluation statistics layer to a ggcyto plot.",
      "topics": [
        "geom_stats"
      ]
    },
    {
      "page": "getFlowFrame",
      "title": "extract flowFrame data structure from the given R object",
      "topics": [
        "getFlowFrame",
        "getFlowFrame.flowSet",
        "getFlowFrame.GatingHierarchy",
        "getFlowFrame.GatingSet",
        "getFlowFrame.GatingSetList",
        "getFlowFrame.ncdfFlowList"
      ]
    },
    {
      "page": "ggcyto_add",
      "title": "overloaded '+' method for ggcyto",
      "topics": [
        "+",
        "+,ggcyto_flowSet,ANY-method",
        "+,ggcyto_flowSet-method",
        "+,ggcyto_GatingLayout,ANY-method",
        "+,ggcyto_GatingLayout-method",
        "+,ggcyto_GatingSet,ANY-method",
        "+,ggcyto_GatingSet-method",
        "+.ggcyto_flowSet",
        "+.ggcyto_GatingLayout",
        "+.ggcyto_GatingSet",
        "+.ggcyto_ncdfFlowList",
        "ggcyto_add"
      ]
    },
    {
      "page": "ggcyto_arrange",
      "title": "Arrange a list of ggplot objects into gtable",
      "topics": [
        "ggcyto_arrange"
      ]
    },
    {
      "page": "ggcyto_par_default",
      "title": "Return The default ggcyto settings",
      "topics": [
        "ggcyto_par_default"
      ]
    },
    {
      "page": "ggcyto_par_set",
      "title": "Set some default parameters for ggcyto",
      "topics": [
        "ggcyto_par_set"
      ]
    },
    {
      "page": "ggcyto",
      "title": "Plot cytometry data using the ggcyto API",
      "topics": [
        "ggcyto",
        "ggcyto-class",
        "ggcyto.default",
        "ggcyto.flowSet",
        "ggcyto.GatingHierarchy",
        "ggcyto.GatingSet",
        "ggcyto.GatingSetList",
        "ggcyto_flowSet-class",
        "ggcyto_GatingLayout-class",
        "ggcyto_GatingSet-class"
      ]
    },
    {
      "page": "is.ggcyto",
      "title": "Reports whether x is a ggcyto object",
      "topics": [
        "is.ggcyto"
      ]
    },
    {
      "page": "is.ggcyto_flowSet",
      "title": "Reports whether x is a ggcyto_flowSet object",
      "topics": [
        "is.ggcyto_flowSet"
      ]
    },
    {
      "page": "is.ggcyto_par",
      "title": "Reports whether x is a ggcyto_par object",
      "topics": [
        "is.ggcyto_par"
      ]
    },
    {
      "page": "labs_cyto",
      "title": "Change axis labels and legend titles",
      "topics": [
        "labs_cyto"
      ]
    },
    {
      "page": "marginalFilter",
      "title": "Generate a marginal gate.",
      "topics": [
        "marginalFilter"
      ]
    },
    {
      "page": "merge.quad.gates",
      "title": "extend the original flowWorkspace:::.mergeGates function to restore quadGate when applicable",
      "topics": [
        "merge.quad.gates"
      ]
    },
    {
      "page": "print.ggcyto",
      "title": "Draw ggcyto on current graphics device.",
      "topics": [
        "plot.ggcyto",
        "print,ggcyto-method",
        "print.ggcyto",
        "show,ggcyto-method",
        "show.ggcyto"
      ]
    },
    {
      "page": "print.ggcyto_GatingLayout",
      "title": "print method for ggcyto_gate_layout class",
      "topics": [
        "print.ggcyto_GatingLayout",
        "show,ggcyto_GatingLayout-method",
        "show.ggcyto_GatingLayout"
      ]
    },
    {
      "page": "replace_data",
      "title": "replace current cytometry data",
      "topics": [
        "%+%",
        "%+%,ggcyto-method",
        "%+%,ggcyto_GatingLayout,ANY-method",
        "%+%,ggcyto_GatingLayout-method",
        "replace_data"
      ]
    },
    {
      "page": "scale_x_flowCore_fasinh",
      "title": "Add a flowCore inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.",
      "topics": [
        "scale_x_flowCore_fasinh",
        "scale_y_flowCore_fasinh"
      ]
    },
    {
      "page": "scale_x_logicle",
      "title": "Add a logicle scale to the x or y axes of a ggcyto plot.",
      "topics": [
        "scale_x_logicle",
        "scale_y_logicle"
      ]
    },
    {
      "page": "scales_flowjo_biexp",
      "title": "Add a flowJo biexponential scale to the x or y axes of a ggcyto plot.",
      "topics": [
        "scales_flowjo_biexp",
        "scale_x_flowJo_biexp",
        "scale_x_flowjo_biexp",
        "scale_y_flowJo_biexp",
        "scale_y_flowjo_biexp"
      ]
    },
    {
      "page": "scales_flowjo_fasinh",
      "title": "Add a flowJo inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.",
      "topics": [
        "scales_flowjo_fasinh",
        "scale_x_flowJo_fasinh",
        "scale_x_flowjo_fasinh",
        "scale_y_flowJo_fasinh",
        "scale_y_flowjo_fasinh"
      ]
    },
    {
      "page": "stat_position",
      "title": "Compute the positions of the population statistics based on the geometic gate centroid for a ggcyto plot.",
      "topics": [
        "stat_position",
        "stat_position.filter",
        "stat_position.filterList",
        "stat_position.list"
      ]
    },
    {
      "page": "stats_null",
      "title": "clear all the geom_stats() layer previously added",
      "topics": [
        "stats_null"
      ]
    },
    {
      "page": "transform-gate",
      "title": "rescale methods for gates",
      "topics": [
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