Package: ggbio 1.55.0
Michael Lawrence
ggbio: Visualization tools for genomic data
The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
Authors:
ggbio_1.55.0.tar.gz
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ggbio.pdf |ggbio.html✨
ggbio/json (API)
NEWS
| # Install 'ggbio' in R: |
| install.packages('ggbio', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lawremi/ggbio/issues
On BioConductor:ggbio-1.55.0(bioc 3.21)ggbio-1.54.0(bioc 3.20)
Last updated 2 months agofrom:289a36c7a2. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | WARNING | Nov 29 2024 |
| R-4.5-linux | WARNING | Nov 29 2024 |
| R-4.4-win | WARNING | Nov 29 2024 |
| R-4.4-mac | WARNING | Nov 29 2024 |
| R-4.3-win | WARNING | Nov 29 2024 |
| R-4.3-mac | WARNING | Nov 29 2024 |
Exports:align.plotsalignPlotsarrangeGrobByParsingLegendautoplotbackupbgColorbgColor<-cbindcirclefixedfixed<-geom_alignmentgeom_archgeom_arrowgeom_arrowrectgeom_bargeom_chevrongeom_rectgeom_segmentggbioGGbioggsavehasAxishasAxis<-heightheight<-Ideogramlabeledlabeled<-layout_circlelayout_karyogrammutablemutable<-nextViewplotFragLengthplotGrandLinearplotIdeogramplotKaryogramplotRangesLinkedToDataplotSpliceSumplotStackedOverviewprevViewrbindrescaleresetscale_fill_fold_changescale_fill_giemsascale_x_sequnitstat_aggregatestat_binstat_coveragestat_genestat_identitystat_mismatchstat_reducestat_slicestat_steppingstat_tabletheme_alignmenttheme_cleartheme_genometheme_noexpandtheme_nulltheme_pack_panelstheme_tracks_sunsettracksxlimxlim<-zoomzoom_inzoom_out
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggplot2ggstatsgluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Arrange grobs by parse their legend. | arrangeGrobByParsingLegend |
| Generic autoplot function | +,Bioplot,Any-method autoplot autoplot,BamFile-method autoplot,BamFileList-method autoplot,BSgenome-method autoplot,character-method autoplot,ExpressionSet-method autoplot,GAlignments-method autoplot,GRanges-method autoplot,GRangesList-method autoplot,IRanges-method autoplot,matrix-method autoplot,OrganismDb-method autoplot,RangedSummarizedExperiment-method autoplot,Rle-method autoplot,RleList-method autoplot,Seqinfo-method autoplot,TabixFile-method autoplot,TxDbOREnsDb-method autoplot,VCF-method autoplot,Views-method autoplot,VRanges-method |
| Alignment geoms for GRanges object | geom_alignment geom_alignment,BamFile-method geom_alignment,GRanges-method geom_alignment,GRangesList-method geom_alignment,missing-method geom_alignment,OrganismDb-method geom_alignment,TxDbOREnsDb-method geom_alignment,uneval-method |
| Arch geoms for GRanges object | geom_arch geom_arch,data.frame-method geom_arch,GRanges-method geom_arch,missing-method geom_arch,uneval-method |
| Arrow geoms for GRanges object | geom_arrow geom_arrow,GRanges-method geom_arrow,missing-method geom_arrow,uneval-method |
| Arrowrect geoms for GRanges object | geom_arrowrect geom_arrowrect,GRanges-method geom_arrowrect,missing-method geom_arrowrect,uneval-method |
| Segment geoms for GRanges object | geom_bar geom_bar,ANY-method geom_bar,chevron-method geom_bar,GRanges-method geom_bar,missing-method |
| Chevron geoms for GRanges object | geom_chevron geom_chevron,GRanges-method geom_chevron,missing-method geom_chevron,uneval-method |
| Rect geoms for GRanges object | geom_rect geom_rect,ANY-method geom_rect,GRanges-method geom_rect,missing-method geom_rect,uneval-method |
| Segment geoms for GRanges object | geom_segment geom_segment,ANY-method geom_segment,GRanges-method geom_segment,missing-method geom_segment,uneval-method |
| class ggbio | $,GGbio-method $<-,GGbio-method +,GGbio,ANY-method GGbio ggbio GGbio-class ggbio-class |
| ggplot methods | ggplot.BSgenome ggplot.character ggplot.ExpressionSet ggplot.GAlignments ggplot.matrix ggplot.RsamtoolsFile ggplot.Seqinfo ggplot.SummarizedExperiment ggplot.TxDbOREnsDb ggplot.VCF ggplot.Vector |
| Save a ggplot object or tracks with sensible defaults | ggsave |
| Grob getter | ggplotGrob-class Grob Grob,gg-method Grob,GGbio-method Grob,gtable-method Grob,lattice-method Grob,trellis-method Grob-class Grob-method GrobList GrobList-class latticeGrob-class |
| Plot single chromosome with cytobands | +,Ideogram,ANY-method Ideogram Ideogram-class plotIdeogram |
| Create a circle layout | circle layout_circle layout_circle,GRanges-method layout_circle,missing-method layout_circle,uneval-method |
| Create a karyogram layout | layout_karyogram layout_karyogram,GRanges-method |
| Plot class | ggbioPlot-class ggplotPlot-class latticePlot-class Plot Plot,gg-method Plot,GGbio-method Plot,Ideogram-method Plot,trellis-method Plot-class |
| Plot estimated fragment length for paired-end RNA-seq data | plotFragLength plotFragLength,character,GRanges-method |
| Manhattan for GWAS | plotGrandLinear |
| Plot Ranges Linked with Data | plotRangesLinkedToData plotRangesLinkedToData,GenomicRanges_OR_GRangesList-method plotRangesLinkedToData,RangedSummarizedExperiment-method |
| Plot Splice Summary from RNA-seq data | plotSpliceSum plotSpliceSum,character,EnsDb-method plotSpliceSum,character,GRangesList-method plotSpliceSum,character,TxDb-method |
| Plot stacked overview | plotKaryogram plotStackedOverview |
| rescale ggplot object | rescale rescale,gg-method rescale,ggplot-method rescale,numeric-method |
| scale color for fold change values | scale_fill_fold_change |
| scale filled color to customized giemsa color. | scale_fill_giemsa |
| scale x by unit | scale_x_sequnit |
| Generates summaries on the specified windows | stat_aggregate stat_aggregate,GRanges-method stat_aggregate,missing-method stat_aggregate,uneval-method |
| Binning method | stat_bin stat_bin,ANY-method stat_bin,missing-method stat_bin,Rle-method stat_bin,RleList-method stat_bin,uneval-method |
| Calculate coverage | stat_coverage stat_coverage,BamFile-method stat_coverage,GRanges-method stat_coverage,GRangesList-method stat_coverage,missing-method stat_coverage,uneval-method |
| Calculate gene structure | stat_gene stat_gene,TxDb-method |
| Transform the data to a data.frame and for multiple geoms. | stat_identity stat_identity,ANY-method stat_identity,GRanges-method stat_identity,missing-method stat_identity,Rle-method stat_identity,RleList-method stat_identity,uneval-method |
| Calculate mismatch summary | stat_mismatch stat_mismatch,BamFile-method stat_mismatch,GRanges-method stat_mismatch,missing-method stat_mismatch,uneval-method |
| Reduce an object. | stat_reduce stat_reduce,GRanges-method stat_reduce,IRanges-method stat_reduce,missing-method stat_reduce,TxDbOREnsDb-method stat_reduce,uneval-method |
| Slice Rle/RleList to view them as bar or heatmap. | stat_slice stat_slice,missing-method stat_slice,Rle-method stat_slice,RleList-method stat_slice,uneval-method |
| Calculate stepping levels | stat_stepping stat_stepping,GRanges-method stat_stepping,missing-method stat_stepping,uneval-method |
| Tabulate a GRanges object | stat_table stat_table,GRanges-method stat_table,GRangesList-method stat_table,missing-method stat_table,uneval-method |
| theme in ggbio | theme_alignment theme_clear theme_genome theme_noexpand theme_null theme_pack_panels theme_tracks_sunset |
| Tracked class | Tracked Tracked-class |
| Tracks for genomic graphics | align.plots alignPlots Arith Arith,Tracks,ANY-method backup backup,Tracks-method bgColor bgColor,gg-method bgColor,GGbio-method bgColor,gtable-method bgColor,Tracked-method bgColor<- bgColor<-,gg,character-method bgColor<-,GGbio,character-method bgColor<-,gtable,character-method bgColor<-,Tracked,character-method c,PlotList-method c,Tracks-method cbind,Tracks-method coerce,Tracks,grob-method fixed,gg-method fixed,GGbio-method fixed,Tracked-method fixed<-,gg,logical-method fixed<-,GGbio,logical-method fixed<-,Tracked,logical-method hasAxis hasAxis,gg-method hasAxis,GGbio-method hasAxis,Tracked-method hasAxis<- hasAxis<-,gg,logical-method hasAxis<-,GGbio,logical-method hasAxis<-,Tracked,logical-method height height,gg-method height,GGbio-method height,Tracked-method height<- height<-,gg,numericORunit-method height<-,GGbio,numericORunit-method height<-,Tracked,numericORunit-method labeled labeled,gg-method labeled,GGbio-method labeled,gtable-method labeled,gTree-method labeled,Ideogram-method labeled,text-method labeled,Tracked-method labeled<- labeled<-,gg,logical-method labeled<-,GGbio,logical-method labeled<-,gtable,logical-method labeled<-,Ideogram,logical-method labeled<-,Tracked,logical-method mutable mutable,gg-method mutable,GGbio-method mutable,Tracked-method mutable<- mutable<-,gg,logical-method mutable<-,GGbio,logical-method mutable<-,Tracked,logical-method print print,Tracks-method rbind,Tracks-method reset reset,Tracks-method show show,Tracks-method summary summary,Tracks-method tracks Tracks-class xlim xlim,GRanges-method xlim,IRanges-method xlim,numeric-method xlim,Tracks-method xlim<- xlim<-,Tracks,GRanges-method xlim<-,Tracks,IRanges-method xlim<-,Tracks,numeric-method [,PlotList,numeric,missing,ANY-method [,Tracks,numeric,missing,ANY-method |
| Simple navigation for ggbio object. | nextView prevView zoom zoom_in zoom_out |
