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 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.