NEWS.md

ggalign (development version)

New features

• 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.

• new geom_subrect() and geom_subtile() to subdivide rectangles with shared borders into a grid.

• new cross_link function used to reset the layout ordering index, this is useful to create tanglegram visualizations.

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, panel will be reordered when initializing the layout parameters, 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

ggalign 0.0.5

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 scheme_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 scheme_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

ggalign 0.0.4

• 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

ggalign 0.0.3

• Add package logo

• new inset() function

• add package quotes in DESCRIPTION

• add return value docs for exported function or methods

ggalign 0.0.2

• omit the redudnant description and add single quote for package name

ggalign 0.0.1

Features

ggalign pacakge provides two layout to arrange ggplot objects:

• heatmap_layout()/ggheatmap(): Arrange ggplot into a Heatmap layout. See vignette("heatmap-layout") for details.

• stack_layout()/ggstack(): Arrange ggplot vertically or horizontally. See vignette("stack-layout") for details.

To further customize these layouts, we offer following functions:

• align_group(): Group layout axis into panel with a group variable.
• align_kmeans(): Group layout axis into panel by kmeans
• align_reorder(): Reorders layout observations based on weights or summary statistics.
• align_dendro(): Reorder or Group layout based on hierarchical clustering

For more detailed instructions on customizing layouts, see the vignette: vignette("layout-customize").

Additionally, plots can be added in the layout with following functions:

• align_gg()/ggalign(): Create ggplot object with a customized data.
• align_panel()/ggpanel(): Create ggplot object with the layout panel data.

For more information on adding plots, refer to the vignette: vignette("layout-plot").