Package: ggalign 1.0.0.9000

ggalign: A 'ggplot2' Extension for Consistent Axis Alignment

A 'ggplot2' extension offers various tools the creation of complex, multi-plot visualizations. Built on the familiar grammar of graphics, it provides intuitive tools to align and organize plots, making it ideal for complex visualizations. It excels in multi-omics research—such as genomics and microbiomes—by simplifying the visualization of intricate relationships between datasets, for example, linking genes to pathways. Whether you need to stack plots, arrange them around a central figure, or create a circular layout, 'ggalign' delivers flexibility and accuracy with minimal effort.

Authors:Yun Peng [aut, cre], Shixiang Wang [aut], Guangchuang Yu [ths]

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ggalign.pdf |ggalign.html✨
ggalign/json (API)
NEWS

# Install 'ggalign' in R:
install.packages('ggalign', repos = c('https://yunuuuu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yunuuuu/ggalign/issues

Pkgdown site:https://yunuuuu.github.io

On CRAN:

Conda:

complex-heatmapsdendrogramdendrogram-heatmapggplotggplot-extensionggplot2heatmapheatmap-visualizationheatmapsmarginal-plotsoncoplotoncoprinttanglegramupsetupsetplot

7.08 score 267 stars 27 scripts 482 downloads 144 exports 28 dependencies

Last updated 2 days agofrom:b8f012ba03. Checks:4 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 16 2025
R-4.5-winOKMar 18 2025
R-4.5-macOKMar 16 2025
R-4.5-linuxOKMar 16 2025
R-4.4-winNOTEMar 16 2025
R-4.4-macNOTEMar 16 2025
R-4.4-linuxNOTEMar 16 2025
R-4.3-winNOTEMar 16 2025
R-4.3-macNOTEMar 16 2025

Exports:.link_draw.mark_drawactivealignAlignalign_dendroalign_groupalign_hclustalign_kmeansalign_orderalign_order2align_panelalign_phyloalign_plotsalignpatchanno_bottomanno_leftanno_rightanno_topareacircle_continuouscircle_discretecircle_layoutcircle_switchcontinuous_limitscoord_circlecross_linkcross_markcross_nonedraw_key_gshapeelement_curveelement_polygonelement_repelement_rep_lenelement_vecelement_vec_recycleelement_vec_repelement_vec_rep_eachelement_vec_slicefacet_sectorfortify_data_framefortify_matrixfree_alignfree_borderfree_guidefree_labfree_spacefree_vpgeom_drawgeom_gshapegeom_piegeom_rect3dgeom_subrectgeom_subtilegeom_tile3dggalignggalign_attrggalign_data_setggalign_lvlsggalign_statggalignGrobggcrossggfreeggheatmapggmarkggoncoplotggpanelggsideggupsetggwrapgparhclust2heatmap_layouthmannoinsetis_circle_layoutis_ggheatmapis_heatmap_layoutis_layoutis_quad_layoutis_stack_crossis_stack_layoutlayer_orderlayout_annotationlayout_designlayout_titlelink_drawlink_linelink_tetragonmark_drawmark_linemark_tetragonmark_trianglememo_ordernew_tuneno_expansionorder2pair_linkspatchpatch_titlesquad_activequad_alignbquad_alignhquad_alignvquad_annoquad_continuousquad_discretequad_freequad_initquad_layoutquad_switchrange_linkraster_magickread_examplescale_gshape_manualscheme_alignscheme_datascheme_themeshowstack_activestack_alignstack_alignhstack_alignvstack_continuousstack_continuoushstack_continuousvstack_crossstack_crosshstack_crossvstack_discretestack_discretehstack_discretevstack_freestack_freehstack_freevstack_horizontalstack_layoutstack_switchstack_verticaltheme_no_axestunetune_dataunitwith_quad

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Define the links to connect a pair of observations.link_draw
Define the links to connect the marked observations.mark_draw
Plot Adding Context Settingsactive
Plot dendrogram treealign_dendro
Group and align observations based on a group vectoralign_group
Reorder or Group observations based on hierarchical clusteringalign_hclust
Split observations by k-means clustering groups.align_kmeans
Order observations based on weightsalign_order
Reorders layout observations based on specific statistics.align_order2
Plot Phylogenetics treealign_phylo
Arrange multiple plots into a gridalign_plots
Define the plotting areas in 'align_plots'area
Arrange plots in a circular layoutcircle_continuous circle_discrete circle_layout
Determine the active context of circle layoutcircle_switch
Set continuous limits for the layoutcontinuous_limits
Polar Coordinates with Enhanced Controlscoord_circle
Add a plot to connect selected observationscross_link
Add a plot to annotate observationscross_mark
Reset layout ordering and panel groupcross_none
Key glyphs for legendsdraw_key_gshape
Theme curve elementselement_curve
Theme Polygon elementselement_polygon
Apply a function to the fields of an element objectelement_rep element_rep_len element_vec element_vec_recycle element_vec_rep element_vec_rep_each element_vec_slice
Polar coordinates with Facet supportfacet_sector
Build a data framefortify_data_frame
Build a data framefortify_data_frame.character fortify_data_frame.complex fortify_data_frame.logical fortify_data_frame.numeric
Build a data framefortify_data_frame.default
Build a data framefortify_data_frame.dendrogram fortify_data_frame.hclust
Build a data framefortify_data_frame.DelayedMatrix fortify_data_frame.Matrix fortify_data_frame.matrix
Build a data framefortify_data_frame.phylo
Build a Matrixfortify_matrix
Build a Matrixfortify_matrix.default
Build a matrix from a maftools objectfortify_matrix.GISTIC
Build a Matrix for UpSet plotfortify_matrix.list fortify_matrix.list_upset
Build a Matrix for OncoPrintfortify_matrix.MAF fortify_matrix.MAF_pathways
Build a matrixfortify_matrix.matrix
Build a Matrix for OncoPrintfortify_matrix.matrix_oncoplot
Build a Matrix for UpSet plotfortify_matrix.matrix_upset
Build a matrix from 'phylo' objectfortify_matrix.phylo
Free from alignmentfree_align free_border free_guide free_lab free_space free_vp
Layer with Grid or Functiongeom_draw
Layer with a customized shape graphic using grid functions.geom_gshape
Pie chartsgeom_pie
Add z-aesthetic for geom_tilegeom_rect3d geom_tile3d
Subdivide Rectanglesgeom_subrect geom_subtile
Add ggplot by Aligning discrete or continuous variableggalign
Get Data from the Attribute Attached by ggalignggalign_attr ggalign_lvls
Attach supplementary data and levels for ggalignggalign_data_set
Get the statistics from the layoutggalign_stat ggalign_stat.QuadLayout ggalign_stat.StackLayout
Generate a plot grob.ggalignGrob
Connect two layout crosswiseggcross
Add ggplot to layout without alignmentggfree ggfree.default
Add a plot to annotate selected observationsggmark
Create an OncoPrintggoncoplot ggoncoplot.default
Create an UpSet plotggupset
Wrap Arbitrary Graphics to ggplotggwrap
Generate Tree Structures with Hierarchical Clusteringhclust2
Create a heatmapggheatmap heatmap_layout
Create a ggplot insetinset
Reports whether 'x' is layout objectis_circle_layout is_ggheatmap is_heatmap_layout is_layout is_quad_layout is_stack_cross is_stack_layout
Change the layer adding orderlayer_order
Modify components of the layoutlayout_annotation
Define the grid to compose plots inlayout_design
Annotate the whole layoutlayout_title
Layout operatorlayout-operator
Define the links to connect a pair of observationslink_draw
Link the paired observations with a linelink_line
Link the paired observations with a quadrilaterallink_tetragon
Define the links to connect the marked observationsmark_draw
Link the observations and the panel with a linemark_line
Link the observations and the panel with a quadrilateralmark_tetragon
Link the observations and the panel with a trianglemark_triangle
Sort matrix for better visualizationmemo_order
Change the shape of the input objectnew_tune tune_data
Remove scale expansionno_expansion
Ordering Permutationorder2 order2.dendrogram order2.hclust order2.memo_weights order2.phylo order2.ser_permutation order2.ser_permutation_vector
Helper function to create pairs of observation groupspair_links range_link
Add patch titles to plot borderspatch_titles
Convert Object into a Grobpatch.alignpatches
Convert Object into a Grobpatch.formula patch.function
Convert Object into a Grobpatch.ggplot
Convert Object into a Grobpatch.gList patch.grob
Convert Object into a Grobpatch.Heatmap patch.HeatmapAnnotation patch.HeatmapList
Convert Object into a Grobpatch.patch
Convert Object into a Grobpatch.patch_ggplot
Convert Object into a Grobpatch.patchwork
Convert Object into a Grobpatch.pheatmap
Convert Object into a Grobpatch.recordedplot
Convert Object into a Grobpatch.trellis
Determine the Active Context of Quad-Layoutanno_bottom anno_left anno_right anno_top quad_active quad_anno
Arrange plots in the quad-side of a main plotggside quad_alignb quad_alignh quad_alignv quad_continuous quad_discrete quad_free quad_layout
Determine the Active Context of Quad-Layouthmanno quad_switch
Rasterize the input objectraster_magick
Read Example Dataread_example
Scale for 'gshape' aestheticscale_gshape_manual
Align Specifications in the Layoutscheme_align
Plot data Specificationsscheme_data
Plot default themescheme_theme
Arrange plots crosswise horizontally or verticallystack_cross stack_crossh stack_crossv
Arrange plots horizontally or verticallystack_align stack_alignh stack_alignv stack_continuous stack_continuoush stack_continuousv stack_discrete stack_discreteh stack_discretev stack_free stack_freeh stack_freev stack_horizontal stack_layout stack_vertical
Determine the active context of stack layoutstack_active stack_switch
Remove axis elementstheme_no_axes
Change the shape of the input objecttune
Convert the shape of a list for fortify methodtune.list
Convert the shape of a MAF for fortify methodtune.MAF
Convert the shape of a matrix for fortify methodtune.matrix
Modify operated Context in 'quad_layout()'with_quad