Changes in version 1.10.0
-------------------------

NEW FEATURES
    
SIGNIFICANT USER-VISIBLE CHANGES
    
BUG-FIXES
    o kpPlotGenes and kpPlotTranscripts no longer flip strands when plotting on
    data.panel=2
    o kpPlotRainfall does not error when a chromosome has no data
    o Fixed inversion bug in plot.type=5




Changes in version 1.10.0
-------------------------

NEW FEATURES
    o Added new color managements functions including is.color and transparent
    and improved the existing ones.
    o Added new functions to color data elements based on different features:
    chromosome, position, overlapping of regions...
    o Improved gene and transcript plotting functions. Added functions to
    automatically get gene symbols from OrgDb objects. Improved transcript
    and gene positioning. Added a function to merge all transcripts of a gene
    into one.
    o kpPlotBigWig can now adjust the ymax value based on the global maximum,
    per chromosome or taking into account only the visible region.

SIGNIFICANT USER-VISIBLE CHANGES
    o It is now posible to add labels to the right-hand side of chromosomes
    with kpAddLabels
    o Improved documentation and vignette
    o makeGenesDataFromTxDb does not need a karyoplot anymore. Changed parameter
    order.
    
BUG-FIXES
    o It is now possible to use cex in plotKaryotype to specify chromosome name sizes 
    o Multiple small bug fixes
    

Changes in version 1.7.17
-------------------------

NEW FEATURES

    o Added autotrack function to automatically assign r0 and r1 values
    o Added kpAddChromosomeSeparators to draw lines between chromosomes
    o Added new plot types: "ideogram" to plot on the ideogram itself and "all" to plot over all data.panels and the ideogram
    o Added kpPlotBigWig to plot data on BigWig files
    o Added regioneR::toGRanges to plotKaryotype zoom, so it's now possible to specify a zoom region with UCSC style region definition (i.e. "chr2:232122-321123")
    o Added colByChr function to assign colors to data elements depending on their chromosome
    
SIGNIFICANT USER-VISIBLE CHANGES

    o Added internal conversion to GenomicRanges using regioneR::toGRanges to kpPlotRegions. It is now possible to directly plot the regions in a BED file, for example.

BUG FIXES

    o Fixed a bug in the coordinate change function where plotting was out of place
    o Fixed a bug in kpPlotCoverage where the coverage would not extend to the end of the chromosome
    o Several minor bug fixes
    


Changes in version 1.7.9
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o New parameter in kpPlotMarkers to allow labels to move beyond the 
    chromosome limits when repositioning to avoid label overlaps


BUG FIXES

    o Fixed a bug in the coordinate change function where plotting was out of place
    or even invisible if the zoom object had addition seqlevels


Changes in version 1.7.4
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The zoom region in plotKaryotype can be specified in any format accepted
    by regioneR::toGRanges, including UCSC/IGV style "chr9:23000-40000".


Changes in version 1.7.3
-------------------------

NEW FEATURES

    o Added `kpPlotBAMCoverage` to plot the exact coverage from a BAM file

SIGNIFICANT USER-VISIBLE CHANGES

    o Improved performance of kpPlotBAMDensity. Specially in zoomed plots.

BUG FIXES

    o kpAxis: Axis were not visible in zoomed plots. They are now visible.


Changes in version 1.7.1
-------------------------

NEW FEATURES

    o Added `kpPlotBigWig` to plot data in bigwig files, usually data derived from BAM coverage for ChIP-seq, etc...

SIGNIFICANT USER-VISIBLE CHANGES

    o Added a `digits` parameter to `kpAddBAseNumbers` to control the number of digits after the decimal point in genome position lables


Changes in version 1.5.4

NEW FEATURES

    o Added `kpPlotGenes` and `kpPlotTranscripts` to plot gene and transcript models
    o Added `kpArea` to plot shaded areas. Ideal for coverage plots, RNA-seq, ChIP-seq, etc...

SIGNIFICANT USER-VISIBLE CHANGES

    o Added plot.type=4 to `plotDefaultPlotParams`
    o Added new examples and extended the tutorial at the karyoploteR tutorial and examples site at https://bernatgel.github.io/karyoploter_tutorial/


BUG FIXES

    o Various minor bug fixes.
    o Various documentation fixes



Changes in version 1.3.11

NEW FEATURES

    o Added zooming to create plots of regions smaller than a whole chromosome. 
    o Added `kpPlotLoess` to plot a fitted loess and confidence interval for data points.
    o Added `kpPlotRainfall` to create rainfall plots from variants.
    o Added `kpPlotLinks` to plot connections between genome regions even in different chromosomes.


SIGNIFICANT USER-VISIBLE CHANGES

    o New default in `plotKaryotype`: now `plot.type` defaults to 1, a ideogram with a single data panel above it


## Other

    o Added unit testing
    o Created a karyoploteR tutorial and examples site at https://bernatgel.github.io/karyoploter_tutorial/


BUG FIXES

    o Fixed a bug causing a misalignment between data points and plotting parameters in some edge cases.
    o Various minor bug fixes.

