NEWS

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Gviz 1.33.1

NEW FEATURES

• score in sashimi plots can be transformed using function specified either in sashimiTransformation or transfromation (latter applied also to coverage)

BUG FIXES

• none

Gviz 1.32.0

NEW FEATURES

• Exposed the possibility to specify centromere shape
• 'AlignmentsTracks' can visualize "indels"
• SequenceTrack has new subclass: SequenceRNAStringSetTrack
• added RNASequenceTrack

BUG FIXES

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

Gviz 1.29.1

NEW FEATURES

• Exposed the possibility to specify width and distance for feather (arrowBar) in AnnotationTrack class

BUG FIXES

• Fixed issue with 'subseq' function for 'ReferenceSequenceTrack'
• Changed the visualized position of tickmarks, and values in 'DataTrack' => align all to + 0.5 position, which matches the 'SequenceTrack' and 'AnnotationTrack' visualization
• Changed the check for transparency support in currently opened device 'supportsAlpha', point moved from center to the left bottom corner

Gviz 1.28.0

BUG FIXES

• Fixed issue with hg19 genome version and BiomartGeneRegionTrack: user needs to provide biomart object pointing to grch37.ensembl.org
• Fixed IdeogramTrack to use user provided title

Gviz 1.20.0

BUG FIXES

• BiomartGeneRegionTracks can now deal with a featureMap list to provide alternative conditional mappings for different Biomarts.

Gviz 1.18.0

BUG FIXES

• Various bug fixes.

Gviz 1.16.0

NEW FEATURES

• AlignmentsTracks will nor use the transformation display parameter to adjust the plotting of the coverage.

Gviz 1.11.0

NEW FEATURES

• BiomartGeneRegionTracks can now be created based on a gene symbol, Ensembl trancript id, Ensebml gene id or ENTREZ gene id.

SIGNIFICANT USER-VISIBLE CHANGES

• Streaming behaviour for BiomartGeneRegionTracks. Already queried regions are cached, and new data is fetched from Biomart on demand.
• Proper handling of UCSC genome identifiers in BiomartGeneRegionTracks. Automated mapping to Ensembl genome versions and Biomart archives.

BUG FIXES

• A number of significant fixes.

Gviz 1.10.0

BUG FIXES

• Various bug fixes.

Gviz 1.9.0

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

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

Gviz 1.8.0

NEW FEATURES

• The new HighlightTrack class to add a comon highlighting region for multiple tracks.
• The new OverlayTrack class to merge the panels of multiple tracks into a single panel.
• The reverseStrand display parameter lets you plot the data relative to the negative strand.
• The just.label display parameter adds control to the placement of group labls in AnnotationTrack and GeneRegionTrack objects.
• The box.legend display parameter to add a box around the legend in a DataTrack object.
• extend.right and extend.left now also take relative expansion factors (as values between -1 and 1).
• A new shape type fixedArrow for AnnotationTrack and GeneRegionTrack objects, and the arrowHeadWidth and arrowHeadMaxWidth parameters to better control the arrow shapes.
• Display parameter schemes to persistently modify parameter settings.
• The new featureAnnotation and groupAnnotation parameters to better control the feature and group labels in AnnotationTracks.
• The new exonAnnotation and transcriptAnnotation parameters to better control the exon and transcript labels in GeneRegionTracks.
• The new AlignmentsTrack class to visualized aligned NGS reads in a BAM file.

BUG FIXES

• A number of significant fixes.

SIGNIFICANT USER-VISIBLE CHANGES

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

Gviz 1.6.0

NEW FEATURES

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

SIGNIFICANT USER-VISIBLE CHANGES

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

Gviz 1.4.0

NEW FEATURES

• BiomartGeneRegionTracks will now make use of the available CDS information in Ensembl.
• 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.
• The mart object in BiomartGeneRegionTrack objects is now cached in order to speed up subsequent queries to the same mart.
• 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.
• Sample names can now be shown in heatmap-type plots by setting the 'showSampleNames' display parameter.

SIGNIFICANT USER-VISIBLE CHANGES

• Complete refactoring of the automatic font size adjustments to provide more reasonable defaults.
• Tick labels on the genomic axis are now show in between tick marks when zoomed in to single nucleotide level.

BUG FIXES

• Fixed a bug in IdeogramTracks where all bands in the rounded caps at the edges of the Ideogram were missing.
• 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.
• Tick labels on the genome axis show only significant digits now.
• Sample ordering in heatmap plots is now correct.
• Numerous little fixes.

Gviz 1.2.0

NEW FEATURES

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

• 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.
• IdeogramTracks can now be constructed from a cytoband table via the new bands argument in the constructor.
• AnnotationTrack objects now by default draw connecting lines in a light gray color. This feature can be controlled via the col.line display parameter.
• Sliding window summarization can now deal with NA values.
• Exporting drawGD from the name space now to allow for sub-classing of GdObjects in other packages.
• When building GeneRegionTracks from TranscriptDb objects the information about UTRs and coding regions is now retained.

BUG FIXES

• When zooming into the emty space between two grouped features, the connecting line will now be plotted for all classes inheriting from AnnotationTrack.
• An error in calculating ylims when drawing AlignedReadTracks has been fixed.
• Numerous other little fixes that mainly aim at improving performance.