| Define the links to connect a pair of observations | .link_draw |
| Define the links to connect the marked observations | .mark_draw |
| Plot Adding Context Settings | active |
| Plot dendrogram tree | align_dendro |
| Group and align observations based on a group vector | align_group |
| Reorder or Group observations based on hierarchical clustering | align_hclust |
| Split observations by k-means clustering groups. | align_kmeans |
| Order observations based on weights | align_order |
| Plot Phylogenetics tree | align_phylo |
| Arrange multiple plots into a grid | align_plots |
| Reorders layout observations based on specific statistics. | align_reorder |
| Define the plotting areas in 'align_plots' | area |
| Arrange plots in a circular layout by aligning continuous axis | circle_continuous |
| Arrange plots in a circular layout by aligning discrete axis | circle_discrete |
| Arrange plots in a circular layout | circle_layout |
| Determine the active context of circle layout | circle_switch |
| Set continuous limits for the layout | continuous_limits |
| Add a plot to connect selected observations | cross_link |
| Add a plot to annotate observations | cross_mark |
| Reset layout ordering and panel group | cross_none |
| Key glyphs for legends | draw_key_draw |
| Key glyphs for legends | draw_key_draw2 |
| Theme curve elements | element_curve |
| Theme Polygon elements | element_polygon |
| Apply a function to the fields of an element object | element_rep element_rep_len element_vec element_vec_recycle element_vec_rep element_vec_rep_each element_vec_slice |
| Build a data frame | fortify_data_frame |
| Build a data frame | fortify_data_frame.character fortify_data_frame.complex fortify_data_frame.logical fortify_data_frame.numeric |
| Build a data frame | fortify_data_frame.default |
| Build a data frame | fortify_data_frame.dendrogram fortify_data_frame.hclust |
| Build a data frame | fortify_data_frame.DelayedMatrix fortify_data_frame.Matrix fortify_data_frame.matrix |
| Build a data frame | fortify_data_frame.phylo |
| Build a Matrix | fortify_matrix |
| Build a Matrix | fortify_matrix.default |
| Build a matrix from a maftools object | fortify_matrix.GISTIC |
| Build a Matrix for UpSet plot | fortify_matrix.list fortify_matrix.list_upset |
| Build a matrix from a maftools object | fortify_matrix.MAF fortify_matrix.MAF_pathways |
| Build a matrix from a matrix | fortify_matrix.matrix |
| Build a Matrix for UpSet plot | fortify_matrix.matrix_upset |
| Build a matrix from 'phylo' object | fortify_matrix.phylo |
| Free from alignment | free_align free_border free_guide free_lab free_space free_vp |
| Layer with Grid or Function | geom_draw |
| Layer with customized draw function | geom_draw2 |
| Pie charts | geom_pie |
| Add z-aesthetic for geom_tile | geom_rect3d geom_tile3d |
| Subdivide Rectangles | geom_subrect geom_subtile |
| Add ggplot by Aligning discrete or continuous variable | ggalign |
| Get Data from the Attribute Attached by ggalign | ggalign_attr ggalign_lvls |
| Attach supplementary data and levels for ggalign | ggalign_data_set |
| Get the statistics from the layout | ggalign_stat ggalign_stat.QuadLayout ggalign_stat.StackLayout |
| Generate a plot grob. | ggalignGrob |
| Connect two layout crosswise | ggcross |
| Add ggplot to layout without alignment | ggfree ggfree.default |
| Add a plot to annotate selected observations | ggmark |
| Create an OncoPrint | ggoncoplot ggoncoplot.default |
| Create an UpSet plot | ggupset |
| Wrap Arbitrary Graphics to ggplot | ggwrap |
| Generate Tree Structures with Hierarchical Clustering | hclust2 |
| Create a heatmap | ggheatmap heatmap_layout |
| Create a ggplot inset | inset |
| Reports whether 'x' is layout object | is_circle_layout is_ggheatmap is_heatmap_layout is_layout is_quad_layout is_stack_cross is_stack_layout |
| Change the layer adding order | layer_order |
| Modify components of the layout | layout_annotation |
| Define the grid to compose plots in | layout_design |
| Annotate the whole layout | layout_title |
| Layout operator | &.CircleLayout &.ggheatmap &.ggside &.HeatmapLayout &.QuadLayout &.StackCross &.StackLayout +.CircleLayout +.ggheatmap +.ggside +.HeatmapLayout +.QuadLayout +.StackCross +.StackLayout -.CircleLayout -.ggheatmap -.ggside -.HeatmapLayout -.QuadLayout -.StackCross -.StackLayout layout-operator |
| Define the links to connect a pair of observations | link_draw |
| Link the paired observations with a line | link_line |
| Link the paired observations with a quadrilateral | link_tetragon |
| Define the links to connect the marked observations | mark_draw |
| Link the observations and the panel with a line | mark_line |
| Link the observations and the panel with a quadrilateral | mark_tetragon |
| Link the observations and the panel with a triangle | mark_triangle |
| Sort matrix for better visualization | memo_order |
| Change the shape of the input object | new_tune tune_data |
| Remove scale expansion | no_expansion |
| Ordering Permutation | order2 order2.dendrogram order2.hclust order2.memo_weights order2.phylo order2.ser_permutation order2.ser_permutation_vector |
| Helper function to create pairs of observation groups | pair_links range_link |
| Add patch titles to plot borders | patch_titles |
| Convert Object into a Grob | patch.alignpatches |
| Convert Object into a Grob | patch.formula patch.function |
| Convert Object into a Grob | patch.ggplot |
| Convert Object into a Grob | patch.gList patch.grob |
| Convert Object into a Grob | patch.Heatmap patch.HeatmapAnnotation patch.HeatmapList |
| Convert Object into a Grob | patch.patch |
| Convert Object into a Grob | patch.patch_ggplot |
| Convert Object into a Grob | patch.patchwork |
| Convert Object into a Grob | patch.pheatmap |
| Convert Object into a Grob | patch.recordedplot |
| Convert Object into a Grob | patch.trellis |
| Determine the Active Context of Quad-Layout | anno_bottom anno_left anno_right anno_top quad_active quad_anno |
| Arrange plots in the quad-side of a main plot by aligning continuous axis | ggside quad_continuous quad_free |
| Arrange plots in the quad-side of a main plot by aligning discrete axis | quad_alignb quad_discrete |
| Arrange plots in the quad-side of a main plot | quad_alignh quad_alignv quad_layout |
| Determine the Active Context of Quad-Layout | hmanno quad_switch |
| Rasterize the input object | raster_magick |
| Read Example Data | read_example |
| Scale for 'draw' aesthetic | scale_draw_manual |
| Align Specifications in the Layout | scheme_align |
| Plot data Specifications | scheme_data |
| Plot default theme | scheme_theme |
| Arrange plots horizontally or vertically by aligning continuous axis | stack_continuous stack_continuoush stack_continuousv stack_free stack_freeh stack_freev |
| Arrange plots crosswise horizontally or vertically | stack_cross stack_crossh stack_crossv |
| Arrange plots horizontally or vertically by aligning discrete axis | stack_align stack_alignh stack_alignv stack_discrete stack_discreteh stack_discretev |
| Arrange plots horizontally or vertically | stack_horizontal stack_layout stack_vertical |
| Determine the active context of stack layout | stack_active stack_switch |
| Remove axis elements | theme_no_axes |
| Change the shape of the input object | tune |
| Convert the shape of a list for fortify method | tune.list |
| Convert the shape of a MAF for fortify method | tune.MAF |
| Convert the shape of a matrix for fortify method | tune.matrix |
| Modify operated Context in 'quad_layout()' | with_quad |
