*_free() layouts have been removed, all layout
has been splitted into two type: align discrete or continous
vairables.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.
fix breaks and labels not work well in discrete scale (#30, #32)
fix wrong results of fortify_matrix.MAF()
method
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
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 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.
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").