_pkgdown.yml

url: https://yunuuuu.github.io/ggalign/

template:
  bootstrap: 5
  light-switch: true

development:
  mode: auto

navbar:
  structure:
    left:  [intro, reference, vignettes, articles, news, benchmarks, faq]
    right: [search, github, lightswitch]
  components:
    benchmarks:
      text: Benchmarks
      href: articles/benchmarks.html
    faq: 
      text: FAQ
      href: articles/FAQ.html

reference:
- title: Layout initialize
  desc: A `Layout` object defines how to place the plots.
  contents:
  - heatmap_layout
  - stack_layout
  - quad_layout
  - cross_align
  - quad_free
  - stack_free
  - ggoncoplot

- title: Layout Building
  desc: >
    All plots begin with a call to `ggheatmap()`/`quad_layout()` or
    `stack_layout()`, supplying default data. You then reorder the observations,
    or split the observations into groups, and add plots, layers, scales, coords
    with `+`. Use `quad_switch()`/`hmanno()` or `stack_switch()` to switch the
    active context. To save a plot to disk, use `ggsave()`.
  contents:
  - layout-operator
  - quad_switch
  - quad_anno
  - with_quad
  - stack_switch
  - active
  - ggalign_attr

- title: Layout Customization
  desc: >
    Fine-tune the arrangement of plots by reordering or splitting axes into separate panels. 
    These functions allow for more detailed customization of plot layouts.
  contents:
  - align_hclust
  - align_group
  - align_kmeans
  - align_order
  - align_reorder

- title: Plot initialize
  desc: >
    This section covers essential functions to add individual plots to the layout, 
    ensuring they align and interact correctly within the defined structure.
  contents:
  - ggfree
  - ggalign
  - align_dendro
  - align_line
  - ggcross

- title: Schemes
  desc: >
    Schemes control the actions of plots in the layout. Scheme can be applied
    either globally to the layout or individually to specific plots.
  contents:
  - scheme_align
  - scheme_data
  - scheme_theme

- title: Extending ggalign
  desc: >
    Functions to enhance and customize the capabilities of ggalign.
  contents:
  - align
  - fortify_data_frame
  - fortify_matrix
  - ggalign_attr_set

- title: Plot composer
  desc: >
    This section outlines essential functions for composing plots into a grid,
    intended for internal use. The core code is derived from the `patchwork`
    package, with the hope of eventually integrating and merging these functions
    into the `patchwork` project.
  contents:
  - align_plots
  - patch_titles
  - free_align
  - free_border
  - free_lab
  - free_space
  - area
  - inset
  - ggwrap
  - layout_design
  - layout_title
  - layout_annotation

- title: Extending Plot Composer
  desc: >
    Extending capabilities to align graphics with `align_plots()`.
  contents:
  - alignpatch
  - patch

- title: Extension of ggplot2
  desc: >
    Extending ggplot2 with additional geoms, scales, and other functionalities.
  contents:
  - geom_pie
  - geom_subrect
  - geom_tile3d
  - theme_no_axes
  - layer_order
  - raster_magick
  - geom_draw
  - scale_draw_manual
  - draw_key_draw
  - theme_ggalign
  - element_polygon

- title: helpers
  desc: A collection of utility functions to enhance usability and functionality.
  contents:
  - ggalignGrob
  - ggalign_stat
  - is_layout
  - hclust2
  - order2
  - dendrogram_data
  - read_example

- title: internal
  contents:
  - starts_with("patch.")
  - starts_with("fortify_matrix.")
  - starts_with("fortify_data_frame.")