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Initialize Layout

A Layout object defines how to place the plots.

stack_layout() stack_horizontal() stack_vertical() stack_discrete() stack_discretev() stack_discreteh() stack_continuous() stack_continuousv() stack_continuoush() stable
Arrange plots horizontally or vertically
quad_layout() quad_alignh() quad_alignv() quad_discrete() quad_continuous() stable
Arrange plots in the quad-side of a main plot
circle_layout() circle_discrete() circle_continuous() experimental
Arrange plots in a circular layout
stack_cross() stack_crossv() stack_crossh() experimental
Arrange plots crosswise horizontally or vertically
heatmap_layout() stable
Create a heatmap
ggoncoplot() stable
Create an OncoPrint
ggupset() experimental
Create an UpSet plot

Build Layout

All plots begin with a call to ggheatmap()/quad_layout() or stack_layout(), supplying default data. You then reorder the observations, or split the observations into groups, and add plots, layers, scales, coords with +. Use quad_switch()/hmanno() or stack_switch() to switch the active context. To save a plot to disk, use ggsave().

quad_switch() hmanno() stable
Determine the Active Context of Quad-Layout
quad_active() quad_anno() anno_top() anno_left() anno_bottom() anno_right() stable
Determine the Active Context of Quad-Layout
with_quad() experimental
Modify operated Context in quad_layout()
stack_switch() stack_active() stable
Determine the active context of stack layout
circle_switch() stable
Determine the active context of circle layout
active() experimental
Plot Adding Context Settings
ggalign_attr() ggalign_lvls()
Get Data from the Attribute Attached by ggalign
continuous_limits()
Set continuous limits for the layout
layout-operator experimental
Layout operator

Customize Layout

Fine-tune the arrangement of plots by reordering or splitting axes into separate panels. These functions allow for more detailed customization of plot layouts.

align_hclust() stable
Reorder or Group observations based on hierarchical clustering
align_group() stable
Group and align observations based on a group vector
align_kmeans() stable
Split observations by k-means clustering groups.
align_order() stable
Order observations based on weights
align_reorder()
Reorders layout observations based on specific statistics.
cross_none()
Reset layout ordering and panel group
memo_order()
Sort matrix for better visualization

Initialize Plot

This section covers essential functions to add individual plots to the layout, ensuring they align and interact correctly within the defined structure.

align_dendro()
Plot dendrogram tree
align_phylo()
Plot Phylogenetics tree
ggfree() experimental
Add ggplot to layout without alignment
ggalign() stable
Add ggplot by Aligning discrete or continuous variable
ggmark()
Add a plot to annotate selected observations
ggcross()
Connect two layout crosswise
cross_mark()
Add a plot to annotate observations
cross_link()
Add a plot to connect selected observations
mark_line()
Link the observations and the panel with a line
mark_tetragon()
Link the observations and the panel with a quadrilateral
mark_triangle()
Link the observations and the panel with a triangle
mark_draw()
Define the links to connect the marked observations
link_line()
Link the paired observations with a line
link_tetragon()
Link the paired observations with a quadrilateral
link_draw()
Define the links to connect a pair of observations
pair_links() range_link()
Helper function to create pairs of observation groups

Schemes

Schemes control the specific behaviour of plots in the layout and can be applied either globally to the layout or individually to specific plots.

scheme_align() experimental
Align Specifications in the Layout
scheme_data() experimental
Plot data Specifications
scheme_theme() experimental
Plot default theme

Extending ggalign

Functions to enhance and customize the capabilities of ggalign.

.mark_draw()
Define the links to connect the marked observations
.link_draw()
Define the links to connect a pair of observations
align() stable
Create a New align Object
fortify_data_frame() stable
Build a data frame
fortify_matrix() stable
Build a Matrix
tune()
Change the shape of the input object
new_tune() tune_data()
Change the shape of the input object
ggalign_data_set()
Attach supplementary data and levels for ggalign
order2()
Ordering Permutation

Plot composer

This section outlines essential functions for composing plots into a grid, intended for internal use. The core code is derived from the patchwork package, with the hope of eventually integrating and merging these functions into the patchwork project.

align_plots()
Arrange multiple plots into a grid
patch_titles()
Add patch titles to plot borders
free_align() free_border() free_guide() free_lab() free_space() free_vp()
Free from alignment
area()
Define the plotting areas in align_plots
inset()
Create a ggplot inset
ggwrap()
Wrap Arbitrary Graphics to ggplot
layout_design()
Define the grid to compose plots in
layout_title()
Annotate the whole layout
layout_annotation()
Modify components of the layout

Extending Plot Composer

Extending capabilities to align graphics with align_plots().

alignpatch()
Prepare plots to be aligned with align_plots
patch()
Convert Object into a Grob

Extension of ggplot2

Extending ggplot2 with additional geoms, scales, and other functionalities.

geom_pie()
Pie charts
geom_subrect() geom_subtile()
Subdivide Rectangles
geom_rect3d() geom_tile3d()
Add z-aesthetic for geom_tile
theme_no_axes()
Remove axis elements
no_expansion()
Remove scale expansion
layer_order()
Change the layer adding order
raster_magick()
Rasterize the input object
geom_draw()
Layer with Grid or Function
draw_key_draw()
Key glyphs for legends
geom_draw2()
Layer with customized draw function
scale_draw_manual()
Scale for draw aesthetic
draw_key_draw2()
Key glyphs for legends
element_polygon()
Theme Polygon elements
element_curve()
Theme curve elements
element_vec() element_rep() element_rep_len() element_vec_recycle() element_vec_rep() element_vec_rep_each() element_vec_slice()
Apply a function to the fields of an element object

helpers

A collection of utility functions to enhance usability and functionality.

ggalignGrob()
Generate a plot grob.
ggalign_stat()
Get the statistics from the layout
is_layout() is_quad_layout() is_stack_layout() is_stack_cross() is_circle_layout() is_heatmap_layout() is_ggheatmap()
Reports whether x is layout object
hclust2()
Generate Tree Structures with Hierarchical Clustering
read_example()
Read Example Data