@@ -1,3 +1,13 @@

+CHANGES IN VERSION 1.33.1

+-------------------------

+NEW FEATURES

+

+    o score in sashimi plots can be transformed using function specified either in 

+      sashimiTransformation or transfromation (latter applied also to coverage)

+      

+BUG FIXES

+    o none 

+

 CHANGES IN VERSION 1.32.0

 -------------------------

 NEW FEATURES

@@ -1,10 +1,11 @@

-CHANGES IN VERSION 1.31.10

+CHANGES IN VERSION 1.32.0

 -------------------------

 NEW FEATURES

     o Exposed the possibility to specify centromere shape

     o `AlignmentsTracks` can visualize "indels"

     o SequenceTrack has new subclass: SequenceRNAStringSetTrack

+    o added RNASequenceTrack

 BUG FIXES

@@ -1,3 +1,16 @@

+CHANGES IN VERSION 1.31.10

+-------------------------

+NEW FEATURES

+

+    o Exposed the possibility to specify centromere shape

+    o `AlignmentsTracks` can visualize "indels"

+    o SequenceTrack has new subclass: SequenceRNAStringSetTrack

+

+BUG FIXES

+

+    o Fixed issue in .buildRange (internal) to correctly build package on windows

+    

+

 CHANGES IN VERSION 1.29.1

 -------------------------

 NEW FEATURES

@@ -1,3 +1,23 @@

+CHANGES IN VERSION 1.29.1

+-------------------------

+NEW FEATURES

+

+    o Exposed the possibility to specify width and distance for

+      feather (arrowBar) in AnnotationTrack class

+

+BUG FIXES

+

+    o Fixed issue with `subseq` function for `ReferenceSequenceTrack`

+

+    o Changed the visualized position of tickmarks, and values in

+      `DataTrack` => align all to + 0.5 position, which matches

+      the `SequenceTrack` and `AnnotationTrack` visualization

+

+    o Changed the check for transparency support in currently opened

+      device `supportsAlpha`, point moved from center to the left

+      bottom corner

+

+

 CHANGES IN VERSION 1.28.0

 -------------------------

 BUG FIXES

@@ -1,3 +1,11 @@

+CHANGES IN VERSION 1.28.0

+-------------------------

+BUG FIXES

+

+    o Fixed issue with hg19 genome version and BiomartGeneRegionTrack:

+      user needs to provide biomart object pointing to grch37.ensembl.org

+    o Fixed IdeogramTrack to use user provided title

+

 CHANGES IN VERSION 1.20.0

 -------------------------

 BUG FIXES

@@ -1,3 +1,16 @@

+CHANGES IN VERSION 1.20.0

+-------------------------

+BUG FIXES

+

+    o BiomartGeneRegionTracks can now deal with a featureMap list to provide

+      alternative conditional mappings for different Biomarts.

+

+CHANGES IN VERSION 1.18.0

+-------------------------

+BUG FIXES

+

+    o Various bug fixes.

+

 CHANGES IN VERSION 1.16.0

 -------------------------

@@ -1,3 +1,12 @@

+CHANGES IN VERSION 1.16.0

+-------------------------

+

+NEW FEATURES

+

+    o AlignmentsTracks will nor use the transformation display

+      parameter to adjust the plotting of the coverage.

+

+

 CHANGES IN VERSION 1.11.0

 -------------------------

@@ -1,3 +1,33 @@

+CHANGES IN VERSION 1.11.0

+-------------------------

+

+NEW FEATURES

+

+    o BiomartGeneRegionTracks can now be created based on a gene

+      symbol, Ensembl trancript id, Ensebml gene id or ENTREZ gene id.

+

+SIGNIFICANT USER-VISIBLE CHANGES

+

+    o Streaming behaviour for BiomartGeneRegionTracks. Already queried

+      regions are cached, and new data is fetched from Biomart on

+      demand.

+

+    o Proper handling of UCSC genome identifiers in

+      BiomartGeneRegionTracks. Automated mapping to Ensembl genome

+      versions and Biomart archives.

+

+BUG FIXES

+

+    o A number of significant fixes.

+

+

+CHANGES IN VERSION 1.10.0

+-------------------------

+

+BUG FIXES

+

+    o Various bug fixes.

+

 CHANGES IN VERSION 1.9.0

 -------------------------

@@ -1,3 +1,15 @@

+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

 -------------------------

@@ -161,7 +173,7 @@ SIGNIFICANT USER-VISIBLE CHANGES

     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,

@@ -174,4 +186,4 @@ BUG FIXES

     o Numerous other little fixes that mainly aim at improving

       performance.

-  

+

@@ -35,6 +35,9 @@ NEW FEATURES

       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.

@@ -1,4 +1,59 @@

-CHANGES IN VERSION 1.4.0

+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.

+

+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

@@ -1,6 +1,20 @@

 CHANGES IN VERSION 1.4.0

 -------------------------

+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

@@ -23,7 +23,31 @@ NEW FEATURES

       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

 -------------------------

@@ -1,4 +1,4 @@

-CHANGES IN VERSION 1.3.2

+CHANGES IN VERSION 1.4.0

 -------------------------

 NEW FEATURES

@@ -16,7 +16,12 @@ NEW FEATURES

       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.  

+      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.

@@ -4,7 +4,19 @@ CHANGES IN VERSION 1.3.2

 NEW FEATURES

     o BiomartGeneRegionTracks will now make use of the available CDS

-    information in Ensembl.

+      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.  

@@ -26,7 +38,6 @@ NEW FEATURES

       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

@@ -46,10 +57,10 @@ SIGNIFICANT USER-VISIBLE CHANGES

     o Exporting drawGD from the name space now to allow for

       sub-classing of GdObjects in other packages.

-    o When building GeneRegionTracks from TrasncriptDb objects, the

+    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,

@@ -1,3 +1,13 @@

+CHANGES IN VERSION 1.3.2

+-------------------------

+

+NEW FEATURES

+

+    o BiomartGeneRegionTracks will now make use of the available CDS

+    information in Ensembl.

+

+

+

 CHANGES IN VERSION 1.2.0

 -------------------------

@@ -11,7 +11,11 @@ NEW FEATURES

       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

new file mode 100644

@@ -0,0 +1,51 @@

+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.

+

+   

+

+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 TrasncriptDb 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.

+

+