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Package index
-
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
-
.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
-
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
-
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