CHANGES IN VERSION 1.9.0
-------------------------

NEW FEATURES

    o The new CustomTrack class to allow for user-defined plotting functions.

SIGNIFICANT USER-VISIBLE CHANGES

    o The collapseTranscripts parameter now offers more control over the type of collapsing.


CHANGES IN VERSION 1.8.0
-------------------------

NEW FEATURES

    o The new HighlightTrack class to add a comon highlighting region
      for multiple tracks.

    o The new OverlayTrack class to merge the panels of multiple
      tracks into a single panel.

    o The reverseStrand display parameter lets you plot the data
      relative to the negative strand.

    o The just.label display parameter adds control to the placement
      of group labls in AnnotationTrack and GeneRegionTrack objects.

    o The box.legend display parameter to add a box around the legend
      in a DataTrack object.

    o extend.right and extend.left now also take relative expansion
      factors (as values between -1 and 1).

    o A new shape type fixedArrow for AnnotationTrack and
      GeneRegionTrack objects, and the arrowHeadWidth and
      arrowHeadMaxWidth parameters to better control the arrow shapes.

    o Display parameter schemes to persistently modify parameter
      settings.

    o The new featureAnnotation and groupAnnotation parameters to
      better control the feature and group labels in AnnotationTracks.

    o The new exonAnnotation and transcriptAnnotation parameters to
      better control the exon and transcript labels in
      GeneRegionTracks.

    o The new AlignmentsTrack class to visualized aligned NGS reads in
      a BAM file.

BUG FIXES

    o A number of significant fixes.


SIGNIFICANT USER-VISIBLE CHANGES

    o Some display parameter names have been reworked, but the old
      ones should still work as aliases.

    o Overplotting in AnnotationTrack and GeneRegionTrack objects has
      been minimized to be able to make better use of alpha
      blending. Also the way composite exons (e.g. part UTR, part CDS)
      are plotted has been changed. Those will now be merged into one
      feature as long as the exon identifier is identical and if they
      can be reduced into a single range wit min.gapwidth=1.


CHANGES IN VERSION 1.6.0
-------------------------

NEW FEATURES

    o The DataTrack class now comes with a new horizon plot type
      thanks to input from Ge Tan.

SIGNIFICANT USER-VISIBLE CHANGES

    o isActiveSeq and isActiveSeq<- are deprecated in GenomicFeatures
      and their methods have been removed from Gviz.


CHANGES IN VERSION 1.4.0
-------------------------

NEW FEATURES

    o BiomartGeneRegionTracks will now make use of the available CDS
      information in Ensembl.

    o The constructors to the AnnotationTrack, GeneRegionTrack,
      DataTrack and SequenceTrack classes now accept a character
      scalar that points to a file on the file system. A number of
      default parser functions have been implemented to read the
      standard file types. Alternatively, a user-defined import
      function can be provided. This feature also supports streaming
      from indexed file types like BAM or bigWig, in which case the
      data is fetched dynamically upon each plotting operation.

    o The mart object in BiomartGeneRegionTrack objects is now cached
      in order to speed up subsequent queries to the same mart.

    o When plotting DataTracks with type 'gradient' or 'heatmap', a
      color scale is plotted next to the regular y-axis to indicate
      the mapping of numeric values in the false color range. Thanks
      to Mark Heron for his code contribution.

    o Sample names can now be shown in heatmap-type plots by setting
      the 'showSampleNames' display parameter.

SIGNIFICANT USER-VISIBLE CHANGES

    o Complete refactoring of the automatic font size adjustments to
      provide more reasonable defaults.

    o Tick labels on the genomic axis are now show in between tick
      marks when zoomed in to single nucleotide level.

BUG FIXES

    o Fixed a bug in IdeogramTracks where all bands in the rounded
      caps at the edges of the Ideogram were missing.

    o The way genomic ranges are plotted is now according to the Lego
      block model suggested by Herve. This is only relevant when zooming
      in to the level of single nucleotides.

    o Tick labels on the genome axis show only significant digits now.

    o Sample ordering in heatmap plots is now correct.

    o Numerous little fixes.

CHANGES IN VERSION 1.2.0
-------------------------

NEW FEATURES

    o A SequenceTrack class has been added to draw genomic sequence
      information on a Gviz plot. Possible inputs for the track are
      DNAStringSet objects or directly from BSgenome packages.

    o GeneRegionTracks can now deal with coding and non-coding regions
      by means of the feature property in combination with the
      thinBoxFeature display parameter.

    o StackedTracks now have a new display parameter 'reverseStacking'
      which reverts the horizontal ordering of stacked items. If set
      to TRUE, the lowest items are moved to the top of the stack, and
      vice versa.

SIGNIFICANT USER-VISIBLE CHANGES

    o Updated the show methods for most tracks to give more meaningful
      and more compact information about the track's
      content. Availablability of data on other chromosomes than the
      currently active one should now be indicated.

    o IdeogramTracks can now be constructed from a cytoband table via
      the new bands argument in the constructor.

    o AnnotationTrack objects now by default draw connecting lines in
      a light gray color. This feature can be controlled via the
      col.line display parameter.

    o Sliding window summarization can now deal with NA values.

    o Exporting drawGD from the name space now to allow for
      sub-classing of GdObjects in other packages.

    o When building GeneRegionTracks from TranscriptDb objects the
      information about UTRs and coding regions is now retained.


BUG FIXES

    o When zooming into the emty space between two grouped features,
      the connecting line will now be plotted for all classes inheriting
      from AnnotationTrack.

    o An error in calculating ylims when drawing AlignedReadTracks has
      been fixed.

    o Numerous other little fixes that mainly aim at improving
      performance.


