# A 'ggplot2' Extension for Composable Visualization

## Documentation for package ‘ggalign’ version 1.1.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D E F G H I L M N O P Q R S T misc

## -- A --

active | Plot Adding Context Settings
align_dendro | Plot dendrogram tree
align_group | Group and align observations based on a group vector
align_hclust | Reorder or Group observations based on hierarchical clustering
align_kmeans | Split observations by k-means clustering groups.
align_order | Order observations based on weights
align_order2 | Reorders layout observations based on specific statistics.
align_phylo | Plot Phylogenetics tree
align_plots | Arrange multiple plots into a grid
anno_bottom | Determine the Active Context of Quad-Layout
anno_left | Determine the Active Context of Quad-Layout
anno_right | Determine the Active Context of Quad-Layout
anno_top | Determine the Active Context of Quad-Layout
area | Define the plotting areas in 'align_plots'

## -- C --

circle_continuous | Arrange plots in a circular layout
circle_discrete | Arrange plots in a circular layout
circle_genomic | Create a Circular Layout for Genomic Data
circle_layout | Arrange plots in a circular layout
circle_switch | Determine the active context of circle layout
continuous_limits | Set continuous limits for the layout
coord_circle | Polar Coordinates with Enhanced Controls
cross_link | Add a plot to connect selected observations
cross_mark | Add a plot to annotate observations
cross_none | Reset layout ordering and panel group

## -- D --

draw_key_gshape | Key glyphs for legends

## -- E --

element_rep | Apply a function to the fields of an element object
element_rep_len | Apply a function to the fields of an element object
element_vec | Apply a function to the fields of an element object
element_vec_fields | Apply a function to the fields of an element object
element_vec_recycle | Apply a function to the fields of an element object
element_vec_rep | Apply a function to the fields of an element object
element_vec_rep_each | Apply a function to the fields of an element object
element_vec_slice | Apply a function to the fields of an element object

## -- F --

facet_sector | Polar coordinates with Facet support
fortify_data_frame | Build a data frame
fortify_data_frame.character | Build a data frame
fortify_data_frame.complex | Build a data frame
fortify_data_frame.default | Build a data frame
fortify_data_frame.DelayedMatrix | Build a data frame
fortify_data_frame.dendrogram | Build a data frame
fortify_data_frame.factor | Build a data frame
fortify_data_frame.GRanges | Build a data frame
fortify_data_frame.hclust | Build a data frame
fortify_data_frame.logical | Build a data frame
fortify_data_frame.Matrix | Build a data frame
fortify_data_frame.matrix | Build a data frame
fortify_data_frame.numeric | Build a data frame
fortify_data_frame.phylo | Build a data frame
fortify_matrix | Build a Matrix
fortify_matrix.default | Build a Matrix
fortify_matrix.GISTIC | Build a matrix from a maftools object
fortify_matrix.list | Build a Matrix for UpSet plot
fortify_matrix.list_upset | Build a Matrix for UpSet plot
fortify_matrix.MAF | Build a Matrix for OncoPrint
fortify_matrix.MAF_pathways | Build a Matrix for OncoPrint
fortify_matrix.matrix | Build a matrix
fortify_matrix.matrix_oncoplot | Build a Matrix for OncoPrint
fortify_matrix.matrix_upset | Build a Matrix for UpSet plot
free_align | Free from alignment
free_border | Free from alignment
free_guide | Free from alignment
free_lab | Free from alignment
free_space | Free from alignment
free_vp | Free from alignment

## -- G --

genomic_density | Calculate Genomic Region Density
genomic_dist | Calculate inter-region distances for genomic rainfall plots
geom_draw | Layer with Grid or Function
geom_gshape | Layer with a customized shape graphic using grid functions.
geom_magick | Draw images as point shapes using magick
geom_pie | Pie charts
geom_rect3d | Add z-aesthetic for geom_tile
geom_subrect | Subdivide Rectangles
geom_subtile | Subdivide Rectangles
geom_tile3d | Add z-aesthetic for geom_tile
ggalign | Add ggplot by Aligning discrete or continuous variable
ggalignGrob | Generate a plot grob.
ggalign_attr | Get Data from the Attribute Attached by ggalign
ggalign_data_set | Attach supplementary data and levels for ggalign
ggalign_lvls | Get Data from the Attribute Attached by ggalign
ggalign_stat | Get the statistics from the layout
ggalign_stat.ggalign::QuadLayout | Get the statistics from the layout
ggalign_stat.ggalign::StackLayout | Get the statistics from the layout
ggcross | Connect two layout crosswise
ggfree | Add ggplot to layout without alignment
ggfree.default | Add ggplot to layout without alignment
ggheatmap | Create a heatmap
ggmark | Add a plot to annotate selected observations
ggoncoplot | Create an OncoPrint
ggoncoplot.default | Create an OncoPrint
ggside | Arrange plots in the quad-side of a main plot
ggupset | Create an UpSet plot
ggwrap | Wrap Arbitrary Graphics to ggplot

## -- H --

hclust2 | Generate Tree Structures with Hierarchical Clustering
heatmap_layout | Create a heatmap
hmanno | Determine the Active Context of Quad-Layout

## -- I --

inset | Create a ggplot inset
is_circle_layout | Reports whether 'x' is layout object
is_ggheatmap | Reports whether 'x' is layout object
is_heatmap_layout | Reports whether 'x' is layout object
is_layout | Reports whether 'x' is layout object
is_quad_layout | Reports whether 'x' is layout object
is_stack_cross | Reports whether 'x' is layout object
is_stack_layout | Reports whether 'x' is layout object

## -- L --

layer_order | Change the layer adding order
layout-operator | Layout operator
layout_design | Define the grid to compose plots in
layout_tags | Control Plot Tagging in Layouts
layout_theme | Modify theme of the layout
layout_title | Annotate the whole layout
link_draw | Define the links to connect a pair of observations
link_line | Link the paired observations with a line
link_tetragon | Link the paired observations with a quadrilateral

## -- M --

magickGrob | Rasterize a grob object with magick
mark_draw | Define the links to connect the marked 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
memo_order | Sort matrix for better visualization

## -- N --

new_tune | Change the shape of the input object
no_expansion | Remove scale expansion

## -- O --

order2 | Ordering Permutation
order2.dendrogram | Ordering Permutation
order2.hclust | Ordering Permutation
order2.memo_weights | Ordering Permutation
order2.phylo | Ordering Permutation
order2.ser_permutation | Ordering Permutation
order2.ser_permutation_vector | Ordering Permutation

## -- P --

pair_links | Helper function to create pairs of observation groups
patch.formula | Convert Object into a Grob
patch.function | Convert Object into a Grob
patch.ggalign::AlignPatches | Convert Object into a Grob
patch.ggplot | Convert Object into a Grob
patch.gList | Convert Object into a Grob
patch.grob | Convert Object into a Grob
patch.Heatmap | Convert Object into a Grob
patch.HeatmapAnnotation | Convert Object into a Grob
patch.HeatmapList | Convert Object into a Grob
patch.patch | Convert Object into a Grob
patch.patchwork | Convert Object into a Grob
patch.patch_ggplot | Convert Object into a Grob
patch.pheatmap | Convert Object into a Grob
patch.recordedplot | Convert Object into a Grob
patch.trellis | Convert Object into a Grob
patch_titles | Add patch titles to plot borders
plot_ideogram | Add an aligned cytoband ideogram plot

## -- Q --

quad_active | Determine the Active Context of Quad-Layout
quad_alignb | Arrange plots in the quad-side of a main plot
quad_alignh | Arrange plots in the quad-side of a main plot
quad_alignv | Arrange plots in the quad-side of a main plot
quad_anno | Determine the Active Context of Quad-Layout
quad_continuous | Arrange plots in the quad-side of a main plot
quad_discrete | Arrange plots in the quad-side of a main plot
quad_free | Arrange plots in the quad-side of a main plot
quad_layout | Arrange plots in the quad-side of a main plot
quad_scope | Modify operated Context in 'quad_layout()'
quad_switch | Determine the Active Context of Quad-Layout

## -- R --

range_link | Helper function to create pairs of observation groups
raster_magick | Rasterize the ggplot layers
read_example | Read Example Data

## -- S --

scale_gshape_manual | Scale for 'gshape' aesthetic
scale_z_binned | z scales
scale_z_continuous | z scales
scale_z_date | z scales
scale_z_datetime | z scales
scale_z_discrete | z scales
scale_z_ordinal | z scales
scheme_align | Align Specifications in the Layout
scheme_data | Plot data Specifications
scheme_theme | Plot default theme
stack_active | Determine the active context of stack layout
stack_align | Arrange plots horizontally or vertically
stack_alignh | Arrange plots horizontally or vertically
stack_alignv | Arrange plots horizontally or vertically
stack_continuous | Arrange plots horizontally or vertically
stack_continuoush | Arrange plots horizontally or vertically
stack_continuousv | Arrange plots horizontally or vertically
stack_cross | Arrange plots crosswise horizontally or vertically
stack_crossh | Arrange plots crosswise horizontally or vertically
stack_crossv | Arrange plots crosswise horizontally or vertically
stack_discrete | Arrange plots horizontally or vertically
stack_discreteh | Arrange plots horizontally or vertically
stack_discretev | Arrange plots horizontally or vertically
stack_free | Arrange plots horizontally or vertically
stack_freeh | Arrange plots horizontally or vertically
stack_freev | Arrange plots horizontally or vertically
stack_genomic | Create a stack Layout for Genomic Data
stack_genomich | Create a stack Layout for Genomic Data
stack_genomicv | Create a stack Layout for Genomic Data
stack_horizontal | Arrange plots horizontally or vertically
stack_layout | Arrange plots horizontally or vertically
stack_switch | Determine the active context of stack layout
stack_vertical | Arrange plots horizontally or vertically

## -- T --

theme_no_axes | Remove axis elements
tune | Change the shape of the input object
tune.list | Convert the shape of a list for fortify method
tune.MAF | Convert the shape of a MAF for fortify method
tune.matrix | Convert the shape of a matrix for fortify method
tune_data | Change the shape of the input object

## -- misc --

.link_draw | Define the links to connect a pair of observations
.mark_draw | Define the links to connect the marked observations