Help Pages of ggbio

• +,ggbio,ANY-method: class ggbio
• +,ideogram,ANY-method: Plot single chromosome with cytoband
• align.plots: Tracks for genomic graphics
• alignPlots: Tracks for genomic graphics
• Arith: Tracks for genomic graphics
• Arith,Tracks,ANY-method: Tracks for genomic graphics
• arrangeGrobByParsingLegend: Arrange grobs by parse their legend.
• autoplot: Generic autoplot function
• autoplot,BamFile-method: Generic autoplot function
• autoplot,BSgenome-method: Generic autoplot function
• autoplot,character-method: Generic autoplot function
• autoplot,ExpressionSet-method: Generic autoplot function
• autoplot,GappedAlignments-method: Generic autoplot function
• autoplot,GRanges-method: Generic autoplot function
• autoplot,GRangesList-method: Generic autoplot function
• autoplot,IRanges-method: Generic autoplot function
• autoplot,matrix-method: Generic autoplot function
• autoplot,Rle-method: Generic autoplot function
• autoplot,RleList-method: Generic autoplot function
• autoplot,Seqinfo-method: Generic autoplot function
• autoplot,SummarizedExperiment-method: Generic autoplot function
• autoplot,TranscriptDb-method: Generic autoplot function
• autoplot,VCF-method: Generic autoplot function
• autoplot,Views-method: Generic autoplot function
• backup: Tracks for genomic graphics
• backup,Tracks-method: Tracks for genomic graphics
• bgColor: Tracks for genomic graphics
• bgColor,gg-method: Tracks for genomic graphics
• bgColor,gtable-method: Tracks for genomic graphics
• bgColor,ideogram-method: Tracks for genomic graphics
• bgColor<-: Tracks for genomic graphics
• bgColor<-,gg,character-method: Tracks for genomic graphics
• bgColor<-,gtable,character-method: Tracks for genomic graphics
• bgColor<-,ideogram,character-method: Tracks for genomic graphics
• coord_genome: coordinate system
• fixed: Tracks for genomic graphics
• fixed,gg-method: Tracks for genomic graphics
• fixed,gtable-method: Tracks for genomic graphics
• fixed,ideogram-method: Tracks for genomic graphics
• fixed<-: Tracks for genomic graphics
• fixed<-,gg,logical-method: Tracks for genomic graphics
• fixed<-,gtable,logical-method: Tracks for genomic graphics
• fixed<-,ideogram,logical-method: Tracks for genomic graphics
• geom_alignment: Alignment geoms for GRanges object
• geom_alignment,GRanges-method: Alignment geoms for GRanges object
• geom_alignment,missing-method: Alignment geoms for GRanges object
• geom_alignment,TranscriptDb-method: Alignment geoms for GRanges object
• geom_alignment,uneval-method: Alignment geoms for GRanges object
• geom_arch: Arch geoms for GRanges object
• geom_arch,data.frame-method: Arch geoms for GRanges object
• geom_arch,GRanges-method: Arch geoms for GRanges object
• geom_arch,missing-method: Arch geoms for GRanges object
• geom_arch,uneval-method: Arch geoms for GRanges object
• geom_arrow: Arrow geoms for GRanges object
• geom_arrow,GRanges-method: Arrow geoms for GRanges object
• geom_arrow,missing-method: Arrow geoms for GRanges object
• geom_arrow,uneval-method: Arrow geoms for GRanges object
• geom_arrowrect: Arrowrect geoms for GRanges object
• geom_arrowrect,GRanges-method: Arrowrect geoms for GRanges object
• geom_arrowrect,missing-method: Arrowrect geoms for GRanges object
• geom_arrowrect,uneval-method: Arrowrect geoms for GRanges object
• geom_bar: Segment geoms for GRanges object
• geom_bar,chevron-method: Segment geoms for GRanges object
• geom_bar,data.frame-method: Segment geoms for GRanges object
• geom_bar,GRanges-method: Segment geoms for GRanges object
• geom_bar,missing-method: Segment geoms for GRanges object
• geom_chevron: Chevron geoms for GRanges object
• geom_chevron,GRanges-method: Chevron geoms for GRanges object
• geom_chevron,missing-method: Chevron geoms for GRanges object
• geom_chevron,uneval-method: Chevron geoms for GRanges object
• geom_rect: Rect geoms for GRanges object
• geom_rect,data.frame-method: Rect geoms for GRanges object
• geom_rect,GRanges-method: Rect geoms for GRanges object
• geom_rect,missing-method: Rect geoms for GRanges object
• geom_rect,uneval-method: Rect geoms for GRanges object
• geom_segment: Segment geoms for GRanges object
• geom_segment,data.frame-method: Segment geoms for GRanges object
• geom_segment,GRanges-method: Segment geoms for GRanges object
• geom_segment,missing-method: Segment geoms for GRanges object
• geom_segment,uneval-method: Segment geoms for GRanges object
• ggbio: class ggbio
• ggbio-class: class ggbio
• ggplot: ggplot generic method
• ggplot,BamFile-method: ggplot generic method
• ggplot,BSgenome-method: ggplot generic method
• ggplot,character-method: ggplot generic method
• ggplot,ExpressionSet-method: ggplot generic method
• ggplot,GappedAlignments-method: ggplot generic method
• ggplot,GRanges-method: ggplot generic method
• ggplot,GRangesList-method: ggplot generic method
• ggplot,IRanges-method: ggplot generic method
• ggplot,matrix-method: ggplot generic method
• ggplot,Rle-method: ggplot generic method
• ggplot,RleList-method: ggplot generic method
• ggplot,Seqinfo-method: ggplot generic method
• ggplot,SummarizedExperiment-method: ggplot generic method
• ggplot,TranscriptDb-method: ggplot generic method
• ggplot,VCF-method: ggplot generic method
• ggplot,Views-method: ggplot generic method
• hasAxis: Tracks for genomic graphics
• hasAxis,gg-method: Tracks for genomic graphics
• hasAxis,gtable-method: Tracks for genomic graphics
• hasAxis,ideogram-method: Tracks for genomic graphics
• hasAxis<-: Tracks for genomic graphics
• hasAxis<-,gg,logical-method: Tracks for genomic graphics
• hasAxis<-,gtable,logical-method: Tracks for genomic graphics
• hasAxis<-,ideogram,logical-method: Tracks for genomic graphics
• height: Tracks for genomic graphics
• height,gg-method: Tracks for genomic graphics
• height,gtable-method: Tracks for genomic graphics
• height,ideogram-method: Tracks for genomic graphics
• height<-: Tracks for genomic graphics
• height<-,gg,numericORunit-method: Tracks for genomic graphics
• height<-,gtable,numericORunit-method: Tracks for genomic graphics
• height<-,ideogram,numericORunit-method: Tracks for genomic graphics
• ideogram-class: Plot single chromosome with cytoband
• labeled: Tracks for genomic graphics
• labeled,gg-method: Tracks for genomic graphics
• labeled,gtable-method: Tracks for genomic graphics
• labeled,gTree-method: Tracks for genomic graphics
• labeled,ideogram-method: Tracks for genomic graphics
• labeled,text-method: Tracks for genomic graphics
• labeled<-: Tracks for genomic graphics
• labeled<-,gg,logical-method: Tracks for genomic graphics
• labeled<-,gtable,logical-method: Tracks for genomic graphics
• labeled<-,ideogram,logical-method: Tracks for genomic graphics
• layout_circle: Create a circle layout
• layout_circle,GRanges-method: Create a circle layout
• layout_circle,missing-method: Create a circle layout
• layout_circle,uneval-method: Create a circle layout
• layout_karyogram: Create a karyogram layout
• layout_karyogram,GRanges-method: Create a karyogram layout
• mold: Mold an object to a data frame
• mold,eSet-method: Mold an object to a data frame
• mold,ExpressionSet-method: Mold an object to a data frame
• mold,GRanges-method: Mold an object to a data frame
• mold,GRangesList-method: Mold an object to a data frame
• mold,IRanges-method: Mold an object to a data frame
• mold,matrix-method: Mold an object to a data frame
• mold,Rle-method: Mold an object to a data frame
• mold,RleList-method: Mold an object to a data frame
• mold,Seqinfo-method: Mold an object to a data frame
• mold,SummarizedExperiment-method: Mold an object to a data frame
• mold,Views-method: Mold an object to a data frame
• mutable: Tracks for genomic graphics
• mutable,gg-method: Tracks for genomic graphics
• mutable,gtable-method: Tracks for genomic graphics
• mutable,ideogram-method: Tracks for genomic graphics
• mutable<-: Tracks for genomic graphics
• mutable<-,gg,logical-method: Tracks for genomic graphics
• mutable<-,gtable,logical-method: Tracks for genomic graphics
• mutable<-,ideogram,logical-method: Tracks for genomic graphics
• plotFragLength: Plot estimated fragment length for paired-end RNA-seq data
• plotFragLength,character,GRanges-method: Plot estimated fragment length for paired-end RNA-seq data
• plotGrandLinear: Manhattan for GWAS
• plotIdeogram: Plot single chromosome with cytoband
• plotKaryogram: Plot stacked overview
• plotRangesLinkedToData: Plot Ranges Linked with Data
• plotSingleChrom: Plot single chromosome with cytoband
• plotSpliceSum: Plot Splice Summary from RNA-seq data
• plotSpliceSum,character,GRangesList-method: Plot Splice Summary from RNA-seq data
• plotSpliceSum,character,TranscriptDb-method: Plot Splice Summary from RNA-seq data
• plotStackedOverview: Plot stacked overview
• print: Tracks for genomic graphics
• print,Tracks-method: Tracks for genomic graphics
• rescale: rescale ggplot object
• rescale,gg-method: rescale ggplot object
• rescale,ggplot-method: rescale ggplot object
• rescale,numeric-method: rescale ggplot object
• reset: Tracks for genomic graphics
• reset,Tracks-method: Tracks for genomic graphics
• scale_fill_fold_change: scale color for fold change values
• scale_fill_giemsa: scale filled color to customized giemsa color.
• scale_x_sequnit: scale x by unit
• show: Tracks for genomic graphics
• show,Tracks-method: Tracks for genomic graphics
• stat_aggregate: Generates summaries on the specified windows
• stat_aggregate,GRanges-method: Generates summaries on the specified windows
• stat_aggregate,missing-method: Generates summaries on the specified windows
• stat_aggregate,uneval-method: Generates summaries on the specified windows
• stat_bin: Binning method
• stat_bin,data.frame-method: Binning method
• stat_bin,missing-method: Binning method
• stat_bin,Rle-method: Binning method
• stat_bin,RleList-method: Binning method
• stat_bin,uneval-method: Binning method
• stat_coverage: Calculate coverage
• stat_coverage,BamFile-method: Calculate coverage
• stat_coverage,GRanges-method: Calculate coverage
• stat_coverage,GRangesList-method: Calculate coverage
• stat_coverage,missing-method: Calculate coverage
• stat_coverage,uneval-method: Calculate coverage
• stat_gene: Calculate gene structure
• stat_gene,TranscriptDb-method: Calculate gene structure
• stat_identity: Transform the data to a data.frame and for multiple geoms.
• stat_identity,data.frame-method: Transform the data to a data.frame and for multiple geoms.
• stat_identity,GRanges-method: Transform the data to a data.frame and for multiple geoms.
• stat_identity,missing-method: Transform the data to a data.frame and for multiple geoms.
• stat_identity,Rle-method: Transform the data to a data.frame and for multiple geoms.
• stat_identity,RleList-method: Transform the data to a data.frame and for multiple geoms.
• stat_identity,uneval-method: Transform the data to a data.frame and for multiple geoms.
• stat_mismatch: Calculate mismatch summary
• stat_mismatch,BamFile-method: Calculate mismatch summary
• stat_mismatch,GRanges-method: Calculate mismatch summary
• stat_mismatch,missing-method: Calculate mismatch summary
• stat_mismatch,uneval-method: Calculate mismatch summary
• stat_reduce: Reduce an object.
• stat_reduce,GRanges-method: Reduce an object.
• stat_reduce,IRanges-method: Reduce an object.
• stat_reduce,missing-method: Reduce an object.
• stat_reduce,TranscriptDb-method: Reduce an object.
• stat_reduce,uneval-method: Reduce an object.
• stat_slice: Slice Rle/RleList to view them as bar or heatmap.
• stat_slice,missing-method: Slice Rle/RleList to view them as bar or heatmap.
• stat_slice,Rle-method: Slice Rle/RleList to view them as bar or heatmap.
• stat_slice,RleList-method: Slice Rle/RleList to view them as bar or heatmap.
• stat_slice,uneval-method: Slice Rle/RleList to view them as bar or heatmap.
• stat_stepping: Calculate stepping levels
• stat_stepping,GRanges-method: Calculate stepping levels
• stat_stepping,missing-method: Calculate stepping levels
• stat_stepping,uneval-method: Calculate stepping levels
• stat_table: Tabulate a GRanges object
• stat_table,GRanges-method: Tabulate a GRanges object
• stat_table,GRangesList-method: Tabulate a GRanges object
• stat_table,missing-method: Tabulate a GRanges object
• stat_table,uneval-method: Tabulate a GRanges object
• summary: Tracks for genomic graphics
• summary,Tracks-method: Tracks for genomic graphics
• theme_alignment: theme in ggbio
• theme_clear: theme in ggbio
• theme_noexpand: theme in ggbio
• theme_null: theme in ggbio
• theme_pack_panels: theme in ggbio
• theme_tracks_sunset: theme in ggbio
• tracks: Tracks for genomic graphics
• Tracks-class: Tracks for genomic graphics
• update: Tracks for genomic graphics
• update,Tracks-method: Tracks for genomic graphics
• xlim: Tracks for genomic graphics
• xlim,GRanges-method: Tracks for genomic graphics
• xlim,IRanges-method: Tracks for genomic graphics
• xlim,numeric-method: Tracks for genomic graphics
• xlim,Tracks-method: Tracks for genomic graphics
• xlim<-: Tracks for genomic graphics
• xlim<-,Tracks,GRanges-method: Tracks for genomic graphics
• xlim<-,Tracks,IRanges-method: Tracks for genomic graphics
• xlim<-,Tracks,numeric-method: Tracks for genomic graphics

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