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"geom_chevron,uneval-method" ] }, { "page": "geom_rect-method", "title": "Rect geoms for GRanges object", "topics": [ "geom_rect", "geom_rect,ANY-method", "geom_rect,GRanges-method", "geom_rect,missing-method", "geom_rect,uneval-method" ] }, { "page": "geom_segment-method", "title": "Segment geoms for GRanges object", "topics": [ "geom_segment", "geom_segment,ANY-method", "geom_segment,GRanges-method", "geom_segment,missing-method", "geom_segment,uneval-method" ] }, { "page": "ggbio-class", "title": "class ggbio", "topics": [ "$,GGbio-method", "$<-,GGbio-method", "+,GGbio,ANY-method", "GGbio", "ggbio", "GGbio-class", "ggbio-class" ] }, { "page": "ggplot-method", "title": "ggplot methods", "topics": [ "ggplot.BSgenome", "ggplot.character", "ggplot.ExpressionSet", "ggplot.GAlignments", "ggplot.matrix", "ggplot.RsamtoolsFile", "ggplot.Seqinfo", "ggplot.SummarizedExperiment", "ggplot.TxDbOREnsDb", "ggplot.VCF", "ggplot.Vector" ] }, { "page": "ggsave", "title": "Save a ggplot object or tracks with sensible defaults", "topics": [ "ggsave" ] }, { "page": "Grob-class", "title": "Grob getter", "topics": [ "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" ] }, { "page": "plotSingleChrom", "title": "Plot single chromosome with cytobands", "topics": [ "+,Ideogram,ANY-method", "Ideogram", "Ideogram-class", "plotIdeogram" ] }, { "page": "layout_circle-method", "title": "Create a circle layout", "topics": [ "circle", "layout_circle", "layout_circle,GRanges-method", "layout_circle,missing-method", "layout_circle,uneval-method" ] }, { "page": "layout_karyogram-method", "title": "Create a karyogram layout", "topics": [ "layout_karyogram", "layout_karyogram,GRanges-method" ] }, { "page": "Plot-class", "title": "Plot class", "topics": [ "ggbioPlot-class", "ggplotPlot-class", "latticePlot-class", "Plot", "Plot,gg-method", "Plot,GGbio-method", "Plot,Ideogram-method", "Plot,trellis-method", "Plot-class" ] }, { "page": "plotFragLength", "title": "Plot estimated fragment length for paired-end RNA-seq data", "topics": [ "plotFragLength", "plotFragLength,character,GRanges-method" ] }, { "page": "plotGrandLinear", "title": "Manhattan for GWAS", "topics": [ "plotGrandLinear" ] }, { "page": "plotRangesLinkedToData", "title": "Plot Ranges Linked with Data", "topics": [ "plotRangesLinkedToData", "plotRangesLinkedToData,GenomicRanges_OR_GRangesList-method", "plotRangesLinkedToData,RangedSummarizedExperiment-method" ] }, { "page": "plotSpliceSum", "title": "Plot Splice Summary from RNA-seq data", "topics": [ "plotSpliceSum", "plotSpliceSum,character,EnsDb-method", "plotSpliceSum,character,GRangesList-method", "plotSpliceSum,character,TxDb-method" ] }, { "page": "plotStackedOverview", "title": "Plot stacked overview", "topics": [ "plotKaryogram", "plotStackedOverview" ] }, { "page": "rescale-method", "title": "rescale ggplot object", "topics": [ "rescale", "rescale,gg-method", "rescale,ggplot-method", "rescale,numeric-method" ] }, { "page": "scale_fill_fold_change", "title": "scale color for fold change values", "topics": [ "scale_fill_fold_change" ] }, { "page": "scale_fill_giemsa", "title": "scale filled color to customized giemsa color.", "topics": [ "scale_fill_giemsa" ] }, { "page": "scale_x_sequnit", "title": "scale x by unit", "topics": [ "scale_x_sequnit" ] }, { "page": "stat_aggregate-method", "title": "Generates summaries on the specified windows", "topics": [ "stat_aggregate", "stat_aggregate,GRanges-method", "stat_aggregate,missing-method", "stat_aggregate,uneval-method" ] }, { "page": "stat_bin-method", "title": "Binning method", "topics": [ "stat_bin", "stat_bin,ANY-method", "stat_bin,missing-method", "stat_bin,Rle-method", "stat_bin,RleList-method", "stat_bin,uneval-method" ] }, { "page": "stat_coverage-method", "title": "Calculate coverage", "topics": [ "stat_coverage", "stat_coverage,BamFile-method", "stat_coverage,GRanges-method", "stat_coverage,GRangesList-method", "stat_coverage,missing-method", "stat_coverage,uneval-method" ] }, { "page": "stat_gene-method", "title": "Calculate gene structure", "topics": [ "stat_gene", "stat_gene,TxDb-method" ] }, { "page": "stat_identity-method", "title": "Transform the data to a data.frame and for multiple geoms.", "topics": [ "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" ] }, { "page": "stat_mismatch-method", "title": "Calculate mismatch summary", "topics": [ "stat_mismatch", "stat_mismatch,BamFile-method", "stat_mismatch,GRanges-method", "stat_mismatch,missing-method", "stat_mismatch,uneval-method" ] }, { "page": "stat_reduce-method", "title": "Reduce an object.", "topics": [ "stat_reduce", "stat_reduce,GRanges-method", "stat_reduce,IRanges-method", 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