new fortify_stack()
function to convert any objects for plot with [ggstack()]
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.
new fortify_heatmap()
method for MAF
object.
plot_action()
gains a new argument inherit
to control the inheritance of data
argument
new ggoncoplot()
function to draw oncoprint
new fortity_heatmap()
function to convert any objects for plot with [ggheatmap()]
align()
, stack_active()
, and hmanno()
functions gain a new argument action
, and deprecate free_guides
, free_spaces
, plot_data
, theme
, free_labs
, and guides
arguments.
new plot_action()
function to control specifications of the plot in layout
merge
function has been implemented with vctrs
for performance
{data.table} is now removed from the dependency
reorder_dendrogram
argument in align_dendro()
function now can accept a function to reorder the tree.
align_dendro()
gain a new argument cutree
to customize the process of tree cutting
for large matrix (> 20000 cells), automatically use geom_raster()
a new layer_order()
function to change the ggplot2 layer adding order
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()
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")
.