Package index • ggalign

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