NEWS

CHANGES IN VERSION 1.19.1
-------------------------

NEW FEATURES

    o autoplot method supports now EnsDb objects and related filter objects.



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.