_pkgdown.yml

destination: docs
reference:
  - title: "The gatingTemplate class"
    desc: >
      The gatingTemplate class represents a gating strategy
      to be applied to a GatingSet, including specifications for
      automated gating methods and names for resulting subpopulations
    contents:
      - gatingTemplate-class
      - gt_gating
      - gt_get_nodes
      - gt_get_gate
      - gt_get_children
      - gt_get_parent
      - gt_get_helpergates
      - gt_toggle_helpergates
      - gt_delete_helpergates
      - as.data.table.gatingTemplate
  - title: "Data-driven methods for generating gates (auto-gating)"
    desc: >
      Use the expression data from a flowFrame 
      to determine gate boundaries and generate gate objects
    contents:
      - gate_flowclust_1d
      - gate_flowclust_2d
      - prior_flowclust
      - gate_mindensity
      - gate_mindensity2
      - gate_quad_sequential
      - gate_quad_tmix
      - gate_quantile
      - gate_tail
      - gate_tautstring
  - title: "Building a gatingTemplate interactively"
    desc: >
      Interactively apply gating methods sequentially as 
      if they were in a gatingTemplate or generate a 
      gatingTemplate based on gating that has already been performed
    contents:
      - gs_add_gating_method
      - gs_remove_gating_method
      - gs_add_gating_method_init
      - gh_generate_template
  - title: "Adding more gating methods"
    desc: >
      Register additional gating methods
      for use in the openCyto framework
    contents:
      - register_plugins
      - gt_list_methods
  - title: "Visualizing gatingTemplates and flowClust results"
    contents:
      - plot,gatingTemplate-method
      - plot,fcTree,character-method
      - plot,fcFilterList,ANY-method
navbar:
  title: openCyto
  right:
    - icon: fas fa fa-github fa-lg
      href: https://github.com/RGLab/openCyto