Package: ggbio 1.61.0

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:Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Sanchit Saini [ctb], Johannes Rainer [ctb]

ggbio_1.61.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggbio/json (API)

# 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-1.61.0(bioc 3.24)ggbio-1.60.0(bioc 3.23)

infrastructure visualization

12.31 score 116 stars 18 packages 908 scripts 53 mentions 71 exports 126 dependencies

Last updated from:5d6ed36bde. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	491
linux-devel-x86_64	NOTE	821
source / vignettes	OK	656
linux-release-x86_64	NOTE	872
macos-release-arm64	NOTE	517
macos-oldrel-arm64	NOTE	469
windows-devel	NOTE	771
windows-release	NOTE	752
windows-oldrel	NOTE	698
wasm-release	OK	395

Exports:align.plots alignPlots arrangeGrobByParsingLegend autoplot backup bgColor bgColor<-cbind circle fixed fixed<-geom_alignment geom_arch geom_arrow geom_arrowrect geom_bar geom_chevron geom_rect geom_segment ggbio GGbio ggsave hasAxis hasAxis<-height height<-Ideogram labeled labeled<-layout_circle layout_karyogram mutable mutable<-nextView plotFragLength plotGrandLinear plotIdeogram plotKaryogram plotRangesLinkedToData plotSpliceSum plotStackedOverview prevView rbind rescale reset scale_fill_fold_change scale_fill_giemsa scale_x_sequnit stat_aggregate stat_bin stat_coverage stat_gene stat_identity stat_mismatch stat_reduce stat_slice stat_stepping stat_table theme_alignment theme_clear theme_genome theme_noexpand theme_null theme_pack_panels theme_tracks_sunset tracks xlim xlim<-zoom zoom_in zoom_out

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray dichromat digest ensembldb evaluate farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue graph gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime nnet openssl OrganismDbi pkgconfig plyr png ProtGenerics R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tinytex UCSC.utils VariantAnnotation vctrs viridisLite withr xfun XML XVector yaml

Part 0: Introduction and quick start

Rendered fromggbio.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

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	+,Tracks,ANY-method +,Tracks,cartesian-method +,Tracks,position_c-method +,Tracks,theme-method +,Tracks,Tracks-method +,Tracks,zoom-method 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

Package: ggbio 1.61.0

ggbio: Visualization tools for genomic data

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