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.
fortify_matrix.MAF() methoddirection 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 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.
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
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
Add package logo
new inset() function
add package quotes in DESCRIPTION
add return value docs for exported function or methods
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 kmeansalign_reorder(): Reorders layout observations based on weights or summary
statistics.align_dendro(): Reorder or Group layout based on hierarchical clusteringFor 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").