_pkgdown.yml

destination: docs
reference:
  - title: "Plot basics"
    desc: >
      The base method, ggcyto, is deliberately designed to mirror the semantics
      of ggplot2, but with added support for cytoverse data structures and layers.
      Where there is no need for function to be extended for the cytoverse 
      (like aes() for adding aesthetic mappings), the ggplot2 versions should 
      function as expected.
    contents:
      - ggcyto-class
      - ggcyto
      - ggcyto.GatingSet
      - ggcyto.flowSet
      - "`+.ggcyto_GatingSet`"
      - "`+.ggcyto_GatingLayout`"
      - "`+.ggcyto_flowSet`"
      - "`%+%`"
      - as.ggplot
      - ggcyto_arrange
  - title: "Added layers"
    desc: >
      geom_gate and geom_overlay are layers for easy addition of the gate
      geometries and additional populations to ggcyto plots.
    contents:
      - geom_gate
      - transform,filter-method
      - geom_overlay
      - geom_hvline
      - geom_stats
      - stat_position
  - title: "Added scales"
    desc: >
      A few additional scaling functions for determining axis scales and labels
    contents:
      - labs_cyto
      - axis_x_inverse_trans
      - axis_y_inverse_trans
      - scale_x_flowCore_fasinh
      - scale_y_flowCore_fasinh
      - scale_x_flowjo_fasinh
      - scale_y_flowjo_fasinh
      - flowCore_asinht_trans
      - scale_x_flowjo_biexp
      - scale_y_flowjo_biexp
      - scale_x_logicle
      - scale_y_logicle
  - title: "Programming with ggcyto"
    desc: >
      These functions provide tools for obtaining information from cytoverse data
      types to aid in constructing plots and also for explicitly
      generating plots
    contents:
      - is.ggcyto
      - is.ggcyto_flowSet
      - is.ggcyto_par
      - getFlowFrame
      - compute_stats
      - marginalFilter
      - print.ggcyto
      - print.ggcyto_GatingLayout
  - title: "Autoplot and fortify"
    desc: >
      autoplot() will quickly generate common default plots according
      for cytoverse data types and fortify() will turn cytoverse data
      types in to data.tables that can be used with ggplot2.
    contents:
      - autoplot
      - fortify
      - fortify.polygonGate
      - fortify.ellipsoidGate
      - fortify.rectangleGate
      - fortify.filterList
      - fortify_fs
  - title: "Controlling ggcyto behavior"
    desc: >
      Specify the ggcyto settings/parameters for a plot or get the default settings
    contents:
      - ggcyto_par_set
      - ggcyto_par_default
navbar:
  title: ggcyto
  right:
    - icon: fas fa fa-github fa-lg
      href: https://github.com/RGLab/ggcyto
figures:
  fig.width: 4.5