Package: ggalign 1.2.0.9000

Yun Peng

ggalign: A 'ggplot2' Extension for Composable Visualization

A 'ggplot2' extension providing an integrative framework for composable visualization, enabling the creation of complex multi-plot layouts such as insets, circular arrangements, and multi-panel compositions. Built on the grammar of graphics, it offers tools to align, stack, and nest plots, simplifying the construction of richly annotated figures for high-dimensional data contexts—such as genomics, transcriptomics, and microbiome studies—by making it easy to link related plots, overlay clustering results, or highlight shared patterns.

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

ggalign_1.2.0.9000.tar.gz
ggalign_1.2.0.9000.zip(r-4.7)ggalign_1.2.0.9000.zip(r-4.6)ggalign_1.2.0.9000.zip(r-4.5)
ggalign_1.2.0.9000.tgz(r-4.6-any)ggalign_1.2.0.9000.tgz(r-4.5-any)
ggalign_1.2.0.9000.tar.gz(r-4.7-any)ggalign_1.2.0.9000.tar.gz(r-4.6-any)
ggalign_1.2.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/docs site:https://yunuuuu.github.io

On CRAN:

Conda:

complex-heatmapsdendrogramdendrogram-heatmapggplotggplot-extensionggplot2heatmapheatmap-visualizationheatmapsmarginal-plotsoncoplotoncoprinttanglegramupsetupsetplot

7.48 score 393 stars 90 scripts 504 downloads 170 exports 17 dependencies

Last updated from:81f417f54b. Checks:7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR304
source / vignettesOK236
linux-release-x86_64ERROR296
macos-release-arm64ERROR247
macos-oldrel-arm64ERROR1604
windows-develERROR287
windows-releaseERROR335
windows-oldrelERROR522
wasm-releaseOK112

Exports:.link_draw.mark_drawactivealignalign_dendroalign_groupalign_hclustalign_kmeansalign_orderalign_order2align_panelalign_phyloalign_plotsalignpatchesanno_bottomanno_leftanno_rightanno_topareaas_grobcircle_continuouscircle_discretecircle_genomiccircle_layoutcircle_switchcontinuous_limitscoord_circleCraftAligncross_linkcross_markcross_nonedraw_key_gshapeelement_repelement_rep_lenelement_vecelement_vec_fieldselement_vec_recycleelement_vec_repelement_vec_rep_eachelement_vec_slicefacet_sectorfortify_data_framefortify_matrixfree_alignfree_borderfree_guidefree_labfree_spacefree_vpgenomic_densitygenomic_distgeom_drawgeom_gshapegeom_magickgeom_piegeom_rect3dgeom_subrectgeom_subtilegeom_tile3dggalignggalign_attrggalign_buildggalign_data_setggalign_gtableggalign_inheritggalign_initggalign_lvlsggalign_statggalign_updateggalignGrobggcrossggfreeggheatmapggmarkggoncoplotggpanelggsideggupsetggwrapgparhclust2heatmap_layouthmannoinsetis_circle_layoutis_ggheatmapis_heatmap_layoutis_layoutis_quad_layoutis_stack_crossis_stack_layoutlayer_orderlayout_annotationlayout_designlayout_tagslayout_themelayout_titlelink_drawlink_linelink_tetragonmagickGrobmark_drawmark_linemark_tetragonmark_trianglememo_ordernew_tuneno_expansionorder2pair_linkspatchPatchpatch_titlepatch_titlesplot_add_schemeplot_ideogramquad_activequad_alignbquad_alignhquad_alignvquad_annoquad_continuousquad_discretequad_freequad_initquad_layoutquad_scopequad_switchrange_linkraster_magickread_examplescale_gshape_manualscale_z_binnedscale_z_continuousscale_z_datescale_z_datetimescale_z_discretescale_z_ordinalSchemescheme_alignscheme_datascheme_themestack_activestack_alignstack_alignhstack_alignvstack_continuousstack_continuoushstack_continuousvstack_crossstack_crosshstack_crossvstack_discretestack_discretehstack_discretevstack_freestack_freehstack_freevstack_genomicstack_genomichstack_genomicvstack_horizontalstack_layoutstack_switchstack_verticaltheme_no_axestunetune_dataunitwith_quad

Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

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 gridalignpatches align_plots
Define the plotting areasarea
Convert Object into a Grobas_grob.formula as_grob.function
Convert Object into a Grobas_grob.ggalign::alignpatches
Convert Object into a Grobas_grob.ggplot
Convert Object into a Grobas_grob.gList
Convert Object into a Grobas_grob.grob
Convert Object into a Grobas_grob.Heatmap as_grob.HeatmapAnnotation as_grob.HeatmapList
Convert Object into a Grobas_grob.patch
Convert Object into a Grobas_grob.patchwork
Convert Object into a Grobas_grob.pheatmap
Convert Object into a Grobas_grob.recordedplot
Convert Object into a Grobas_grob.trellis
Create a Circular Layout for Genomic Datacircle_genomic
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
Apply a function to the fields of an element objectelement_rep element_rep_len element_vec element_vec_fields 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.factor 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.GRanges
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
Free plots from alignment constraintsfree_align free_border free_guide free_lab free_space free_vp
Calculate Genomic Region Densitygenomic_density
Calculate inter-region distances for genomic rainfall plotsgenomic_dist
Layer with Grid or Functiongeom_draw
Layer with a customized shape graphic using grid functions.geom_gshape
Draw images as point shapes using magickgeom_magick
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
Build a Graphical Object for Renderingggalign_build
Attach supplementary data and levels for ggalignggalign_data_set
Convert a Built Object into a gtableggalign_gtable
Inherit Properties from Another Objectggalign_inherit
Initialize the Default Properties of an Objectggalign_init
Get the statistics from the layoutggalign_stat ggalign_stat.ggalign::QuadLayout ggalign_stat.ggalign::StackLayout
Update the Properties of an Objectggalign_update
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
Define the grid to compose plots inlayout_design
Control Plot Tagging in Layoutslayout_tags
Modify theme of the layoutlayout_theme
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
Rasterize a grob object with magickmagickGrob magickGrob.grob magickGrob.magickGrob
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_title patch_titles
Patch objectPatch Patch-ggproto
Add an aligned cytoband ideogram plotplot_ideogram
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
Modify operated Context in 'quad_layout()'quad_scope
Determine the Active Context of Quad-Layouthmanno quad_switch
Rasterize the ggplot layersraster_magick
Read Example Dataread_example
Scale for 'gshape' aestheticscale_gshape_manual
z scalesscale_z_binned scale_z_continuous scale_z_date scale_z_datetime scale_z_discrete scale_z_ordinal
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
Create a stack Layout for Genomic Datastack_genomic stack_genomich stack_genomicv
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