CHANGES IN VERSION 1.5.16 ------------------------ NEW FEATURES o ggplot generic method added. o mold generic method added for molding object to data.frame. o support ggplot(data) + stat_* style, original data being kept. o tracks function updated, API is enhenced, utilities could control attributes of plots and trakcs. o autoplot now support: VCF, SummarizedExperiments, matrix, where when genomic position is provided, options to visualize a heatmap sitting on the genomic position. o theme could define track based themes. o ideogram: support + xlim method, when embeded with tracks, automatically update zoomed region. o pheno.plot added to SuumarizedExperiemnts and ExpressionSet. SIGNIFICANT USER-LEVEL CHANGES o align.plots is deprecated, alignPlots created Notes o updated website for ggbio: http://tengfei.github.com/ggbio manuals and vignettes and paper added CHANGES IN VERSION 1.1.8 ------------------------ NEW FEATURES o create lower level API and rewrite higher level API o new geom: geom_alignment, geom_chevron, geom_arch, geom_arrow, geom_arrowrect o redefined geom: geom_rect, geom_segment o new stat: stat_aggregate, stat_coverage, stat_mismatch, stat_gene, stat_table, stat_stepping o redefined stat: stat_identity o new layout: layout_circle, layout_karyogram o tracks function are more smart and with more accessors. o themes provided. o More supported object for autoplot: VCF, ExpressionSet, GenomicRangesList. SIGNIFICANT USER-LEVEL CHANGES o qplot changed to generic autoplot function. o argument use only "facets", no alias "facet_gr" or "facet" accepted. o plotMismatchSum will be replaced by stat_mismatch, or autoplot, BamFile. Notes o new website for ggbio: http://tengfei.github.com/ggbio hosting docs, tutorials and case study o pdf version vignette will not longer supported or just provide a short form.