* Fixed alignment of absolute panel dimensions when using `theme(panel.widths, panel.heights)` in ggplot2 v4.0.0. * 'alignpatch-*' scripts have been fully refactored with S7 classes, with more informative and consistent naming. * Improved `align_plots()` to properly handle strips with different placements. * Renamed the original `alignpatch()` to `patch()` for clearer and more consistent naming. * The `Patch` object is now exported for external use. * Refactored `patch_titles` to the new S7-based `patch_title` class (soft-deprecated the old version). * Renamed the original `patch()` to `as_grob()` for clearer.

The internal structure has been fully refactored, with more informative and consistent naming. * remove `element_polygon()`/`element_curve()`, to be implemented upstream in ggplot2 * new `layout_theme()` to control layout theming. * Deprecated the `theme` argument in `layout_annotation()`. * Migrated all internal objects to the S7 class system. * replace `with_quad()` with `quad_scope()` and deprecate old name. * new `layout_tags()`: add support for tagging plots and nested layouts. * `&` operator now can work for `align_plots()`. * new `geom_magick()` object to draw images as point shapes using magick * The `sector_spacing` argument in `facet_sector()` can be a multi-value numeric (#73) * new argument `split` in `align_phylo()` to support splitting phylo objects into multiple trees (#74) * The `fortify_matrix()` method for `phylo` object is removed * new `plot_ideogram()` function to add an aligned cytoband ideogram plot

* `align_plots()`: Always ensure that plots placed in a border collect their guides, if any guides are to be collected in that border. This prevents overlap, unless the guides will be collected by the parent layout. * new scale for z aesthetic: scale_z_continuous, scale_z_binned, scale_z_discrete, scale_z_ordinal, scale_z_datetime, scale_z_date * `geom_subrect()` and `geom_subtile()` gain `nrow` and `ncol` arguments to control the layout, and deprecate `direction` argument * `ggoncoplot()` gains a new argument `remove_duplicates` to control whether to remove duplicated variants within the same cell. * `fortify_data_frame.matrix()` gains a new argument `lvls`, allowing matrix values to be converted into a factor. * `circle_layout()`: fix wrong `sector_spacing` due to the operator precedence when building. * `circle_layout()`: rename `spacing_theta` argument to `sector_spacing` argument, and deprecate `spacing_theta` argument. * `circle_continous`: gains `spacing_theta` argument to control the sector spacing for all plots. * `facet_sector()`: deprecate `radial` argument, user should add the `coord_radial()` or `coord_circle()` directly to the plot. * new `magickGrob()` to construct grob with `magick` processing.

* fix R CMD check error for the updated version of ggplot2 3.5.2. * new grob `channelGrob()` used to create grobs across different facet. * fix `patch.gList` method.

This is a major release. While not many new features have been added, this marks the first release where the entire layout system has been completed. ## Breaking changes * align_reorder() has been renamed to align_order2(). * geom_draw2() has been renamed to geom_gshape(). ## New features * Now `circle_layout()` support multiple facets. * new `facet_sector()` function to add Facet support for polar coordinates * new `coord_circle()` function to provide additional customization options for coord_radial() * new `tune()` method shape ("oncoplot") for matrix

## Breaking changes * Now, all `*_free()` layouts have been removed, all layout has been splitted into two type: align discrete or continous vairables. ## New features * new helper function `memo_order()` to reorder the oncoplot samples. * new `geom_subrect()` and `geom_subtile()` to subdivide rectangles with shared borders into a grid. * new `cross_link` function to reset the layout ordering index or layout panel group, and add plot to connect selected observations. * new `cross_mark` function to reset the layout ordering index or layout panel group, and add plot to annotate observations. * new `pair_links()` function to create pairs of observation groups. * new `mark_draw()`, `mark_line()`, `mark_tetragon()` to define the links to connect the marked observations. * new `link_draw()`, `link_line()`, `link_tetragon()` to define the links to connect a pair of observations * new `ggmark()` to add a plot to annotate selected observations. * new `element_vec()` functions to apply function to the vectorized fields of the theme element object. * new `no_expansion()` function to remove scale expansion. * new layout `circle_layout()` to arrange plot in a circular. * new `raster_magick()` function to post-processing the image raster with `magick` package was added. * new `fortify_matrix.GISTIC()` method for `GISTIC` object from `maftools` package (#24). * `+` operator now will respect `with_quad()`. * new `ggalign_attr_set()` and `ggalign_attr_get()` for basic operations of attached attribute. * new `geom_draw()` function to draw ggplot2 layer with customized draw function. ## Bug fixes * fix breaks and labels not work well in discrete scale (#30, #32) * fix wrong results of `fortify_matrix.MAF()` method ## Improvements * Now, `with_quad()` wraps the object into a list with the class `with_quad`. This approach offers greater flexibility in defining the actions associated with `with_quad`, allowing for more customizable behavior (#26, @Yunuuuu). * Now, we always set as.table = FALSE when using ggplot2 `facet_*()` functions, we don't need to reorder the `panel` when drawing. * `free_gg`, `align` and the new `cross_link` objects have been collapsed to one class `ggalign_plot`

## Breaking changes * `direction` argument in `stack_layout()`/`ggstack()` is soft-deprecated now, user must provide it manually. * `set_context`, `order`, and `name` arguments in `align_*()` and `ggheatmap()` are soft-deprecated, which is advised to use `active` argument. * `guides`, `free_guides`, `free_spaces`, `free_labs`, and `plot_data` arguments in `align_*()` and `ggheatmap()` are deprecated, which is advised to use `plot_align` function instead. * `theme` argument in `align_*()` and `ggheatmap()` is deprecated, which is advised to use `plot_theme` function. * `what` argument in `stack_active()` is soft-deprecated, user is advised to use `stack_switch()` to change the active plot with `what`. * `align_panel()`/`ggpanel()` is deprecated, user is advised to use `ggalign(data = NULL)` instead. ## New features * new `quad_layout()` to create layout allowing free from alignment. * new `quad_alignv()`, `quad_alignh()`, `quad_free()`/`ggside()`, `quad_alignb()` alias for `quad_layout()`. * `stack_layout()` now gains a `type` argument to control whether the layout should align observations. * new `ggoncoplot()` function to draw oncoprint. * new `ggfree()` function to add ggplot to the layout. * new `fortify_matrix()` function to convert any objects to a matrix, and add `fortify_matrix()` method for `MAF` object. * new `fortify_data_frame()` function to convert any objects to a data frame. * now, a special attribute `ggalign` can be used to pass additional informations across the building process, and a new function `ggalign_attr()` can be used to extract the data from the attribute. * new `plot_theme()` function to control the default theme of the plot in layout. * new `plot_data()` function to control the data transformation of the plot in layout. * new `plot_align()` function to control specifications of the plot in layout. * new `with_quad()` function to control the `-` operator context. * new `quad_init()` function to initialize the annotation with self-provided data. * new `stack_switch()` and `quad_switch()` to switch active plots for `stack_layout()` and `quad_layout()`. * new `anno_top()`, `anno_left()`, `anno_bottom()` and `anno_right()` alias for add annotation in `quad_layout()`. * `align_dendro()` gain a new argument `cutree` to customize the process of tree cutting. * `reorder_dendrogram` argument in `align_dendro()` function now can accept a function to reorder the tree. * new `layer_order()` function to change the ggplot2 layer adding order. * new `theme_no_axes()` function to remove axis elements. * new `geom_pie()` function to draw pie charts. ## Bug fixes * fix bug when apply `free_border` in `alignpatches` object. * fix bug when provide a function in `distance` argument of `align_dendro()` * fix bug when provide `hclust` or `dendrogram` in method argument of `align_dendro()` * fix bug of `coord_ggalign()` for discrete scale ## Improvements * `merge` function has been implemented with `vctrs` for performance * for large matrix (> 20000 cells), automatically use `geom_raster()` * {data.table} is now removed from the dependency

* `layout_heatmap()`/`ggheatmap()` arguments width/height have been renamed `.width`/`.height` to helps avoid conflicts with arguments from `geom_tile()`. * the nestet alignpatches theme by default will inherit from the parent alignpatches * new `layout_title()` function, now `layout_annotation()` only control the layout theme * add `ggrastr::rasterize` method for both `ggheatmap()` and `ggstack()` * `set_context` argument in `align_dendro()` now depends on `plot_dendrogram` by default * `align_dendro()` gain a new argument `reorder_dendrogram` to control whether to reorder the generated dendrogram based on the mean values. * `align_reorder()` now splitted into two function `align_order()` and `align_reorder()` * `dendrogram_data()` gain a new argument `reorder_branches` to control whether to reorder the input `leaf_braches` based on the tree. * `align_dendro()` gain new argument `merge_dendrogram` to control whether the dendrograms in multiple groups should be merged * dendrogram height axis will be automatically reversed in bottom and left annotation stack * heatmap fill color scale now default use `scale_fill_gradient2(low = "blue", high = "red")` for continuous values. * `Coord` is used to set limits instead of `Scale` * all `free_*` arguments now accept the same argument of the corresponding `free_*` functions. * new `theme_ggalign()` function for the default theme of ggalign package * export option `ggalign.default_theme` allow user to change the global default theme * new `free_guide()` function, to override the layout guides argument for single plot * `geom_draw()` now utilize `patch()` function to convert objects into grob * internal changes: all vectors have been operated with `vctrs` package * `stack_layout()`: gain `sizes` argument to control the relative sizes of the stack * `align_()*`: now `order` argument only control the plot area. * `align_reorder()` now can accept an ordering character names. * export `order2()` function * `align_reorder()`: fun argument has been renamed to `order` argument, and it can now accept the ordering integer index directly * `fun` in `align_reorder()` now can return any statistics which can be handled by `order2()` * fix `ggheatmap()` order not work when put in a stack layout * `method` in `hclust2()` can now return any objects which can be coerced into hclust, or you can provide such object directly in `method`. * `hclust2()` now can accept `distance = NULL` * `hmanno()`, `stack_active()`, and `align_*()` functions gain a new argument `theme` to control the theme for the plot. * new `layout_annotation()` and `layout_theme()` to modify the layout components * `borders` argument in `free_space()` has been renamed to `spaces` * {tibble} is now removed from the dependency * `align_plots()` now can accept `gList`, `function`, `recordedplot`, `trellis`, `pheatmap`, `Heatmap`, `HeatmapAnnotation`, and `HeatmapList`, we have added `alignpatch` method for these objects. * add `patch` method for `gList`, `function`, `recordedplot`, `trellis`, `pheatmap`, `Heatmap`, `HeatmapAnnotation`, and `HeatmapList` * fix a bug in `wrap()` function where duplicated names in gtable cause some grobs missing * new `free_vp()` function to customize the viewport when aligning. * `StackLayout` and `HeatmapLayout` methods have been collapsed into one method for `Layout` class * New `Patch` class, now we can extend the alignment process of any object and customize the building process with `ggproto`. * fix missing variable `labs` in the `free_space` method of `PatchAlignpatches`