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").