# A 'ggplot2' Extension for Consistent Axis Alignment

## Documentation for package ‘ggalign’ version 0.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A D F G H I L O P Q R S T W misc

## -- A --

active | Plot Adding Context Settings
align_dendro | Reorder or Group observations based on hierarchical clustering
align_gg | Create ggplot object
align_group | Group and align observations based on a group vector
align_kmeans | Split observations by k-means clustering groups.
align_order | Order observations based on weights
align_plots | Arrange multiple plots into a grid
align_reorder | Reorders layout observations based on specific statistics.
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'

## -- D --

dendrogram_data | Dengrogram x and y coordinates

## -- F --

fortify_data_frame | Build a data frame
fortify_data_frame.character | Build a data frame
fortify_data_frame.default | Build a data frame
fortify_data_frame.matrix | Build a data frame
fortify_data_frame.numeric | Build a data frame
fortify_matrix | Build a Matrix
fortify_matrix.default | Build a Matrix
fortify_matrix.MAF | Build a Matrix
fortify_stack | Build data for the stack layout
free_align | Free from alignment
free_border | Free from alignment
free_gg | Add ggplot to layout
free_guide | Free from alignment
free_lab | Free from alignment
free_space | Free from alignment
free_vp | Free from alignment

## -- G --

geom_pie | Pie charts
ggalign | Create ggplot object
ggalignGrob | Generate a plot grob.
ggalign_attr | Get data from the 'ggalign' attribute
ggalign_stat | Get the statistics from the layout
ggalign_stat.QuadLayout | Get the statistics from the layout
ggalign_stat.StackLayout | Get the statistics from the layout
ggfree | Add ggplot to layout
ggheatmap | Arrange Plots in a Heatmap
ggoncoplot | Create 'OncoPrint' Visualizations from Genetic Alteration Data
ggoncoplot.default | Create 'OncoPrint' Visualizations from Genetic Alteration Data
ggside | Arrange Plots in the Quad-Side of a main plot
ggstack | Put plots horizontally or vertically
ggwrap | Wrap Arbitrary Graphics to ggplot

## -- H --

hclust2 | Generate Tree Structures with Hierarchical Clustering
heatmap_layout | Arrange Plots in a Heatmap
hmanno | Determine the Active Context of Quad-Layout

## -- I --

inset | Create a ggplot inset
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_layout | Reports whether 'x' is layout object

## -- L --

layer_order | Change the layer adding order
layout-operator | Layout operator
layout_annotation | Modify components of the layout
layout_design | Define the grid to compose plots in
layout_title | Annotate the whole layout

## -- O --

Ops-method | Layout operator
order2 | Ordering Permutation
order2.dendrogram | Ordering Permutation
order2.hclust | Ordering Permutation
order2.ser_permutation | Ordering Permutation
order2.ser_permutation_vector | Ordering Permutation

## -- P --

patch.alignpatches | Convert Object into a Grob
patch.formula | Convert Object into a Grob
patch.function | 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_align | Align Specifications in the Layout
plot_data | Plot data Specifications
plot_theme | Plot default theme

## -- 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_free | Arrange Plots in the Quad-Side of a main plot
quad_init | Initialize Quad-Layout Annotation
quad_layout | Arrange Plots in the Quad-Side of a main plot
quad_switch | Determine the Active Context of Quad-Layout

## -- R --

read_example | Read Example Data

## -- S --

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_free | Arrange Plots Horizontally or Vertically
stack_freeh | Arrange Plots Horizontally or Vertically
stack_freev | Arrange Plots Horizontally or Vertically
stack_layout | Put plots horizontally or vertically
stack_switch | Determine the active context of stack layout

## -- T --

theme_ggalign | Theme for Layout Plots
theme_no_axes | Remove axis elements

## -- W --

with_quad | Modify Context for the '-' Operator in 'quad_layout()'

## -- misc --

&.ggheatmap | Layout operator
&.ggside | Layout operator
&.HeatmapLayout | Layout operator
&.QuadLayout | Layout operator
&.StackLayout | Layout operator
+.ggheatmap | Layout operator
+.ggside | Layout operator
+.HeatmapLayout | Layout operator
+.QuadLayout | Layout operator
+.StackLayout | Layout operator
-.ggheatmap | Layout operator
-.ggside | Layout operator
-.HeatmapLayout | Layout operator
-.QuadLayout | Layout operator
-.StackLayout | Layout operator