Changes in version 1.0.17                        

BUG FIXES

  - ENTREZ IDs obtained from AnnotationDbi::select() are subset just for
    ENTREZID column when determining default gene priorities,
    eliminating dplyr incompatible types error.
  - All plus and minus strand gene name label parsing in plotGenes is
    now carried out only if there is a non-zero number of that strand's
    genes.

                       Changes in version 1.0.16                        

  - Citation linked for plotgardener publication in Bioinformatics.

                       Changes in version 1.0.15                        

BUG FIXES

  - plotSignal yrange parsing for negative scores now has fixed the typo
    on line 418 from "score2" to "score".

                       Changes in version 1.0.14                        

BUG FIXES

  - plotSignal default yrange parsing now catches the invalid 0,0 range
    and no longer throws a viewport related error.

                       Changes in version 1.0.13                        

BUG FIXES

  - readHic and functions related to the reading of .hic files now
    leaves the chromosome input formatted as is (e.g. "chr1" and "1").
    Functions will throw an error if the input chromosome is not found
    in the chromosomes listed in the .hic file.

                       Changes in version 1.0.12                        

BUG FIXES

  - annoDomains coordinates fixed for plotHicRectangle.
  - Clipping logic for plotPairsArches now clips arches both on left and
    right side of plot.
  - Subsetting plotPairs logic fixed to match plotPairsArches.

NEW FEATURES

  - clip.noAnchors parameter in plotPairsArches allows for inclusion or
    clipping of arches that do not have anchors in the given genomic
    region.
  - plotPairsArches now allows for column name input to designate
    archHeights.

                       Changes in version 0.99.11                       

BUG FIXES

  - : added back to readHic for strawr region parsing.
  - plotHicSquare subsetting fixed for off diagonal regions.

NEW FEATURES

  - All Hi-C functions now allow input of remote Hi-C files.

                       Changes in version 0.99.9                        

This package was previously called BentoBox.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Version bump to 0.99.0 for Bioconductor package submission.
  - bb_mapColors function for users to map a vector to a palette of
    colors.
  - linecolor parameter in bb_plotPairs, bb_plotPairsArches, and
    bb_plotRanges now accepts a single value, a vector of colors, a
    colorby object, or the value "fill".

                      Changes in version 0.0.0.14                       

BUG FIXES

  - R version requirement changed to (R >= 4.1.0) for proper plot
    placement.

NEW FEATURES

  - colorby object now has a scalePerRegion parameter to scale numerical
    colorby data to the range of data in a plotted genomic region.

                      Changes in version 0.0.0.13                       

SIGNIFICANT USER-VISIBLE CHANGES

  - bb_plotManhattan fill paramete now accepts a single value, a vector
    of colors, or a colorby object.

                      Changes in version 0.0.0.12                       

SIGNIFICANT USER-VISIBLE CHANGES

  - colorby constructor now includes optional palette specification.
  - bb_plotPairs, bb_plotPairsArches, and bb_plotRanges fill parameter
    now accepts a single value, a vector of colors, or a colorby object.

BUG FIXES

  - GInteractions assembly match checking moved before dataframe
    conversion.

                      Changes in version 0.0.0.11                       

SIGNIFICANT USER-VISIBLE CHANGES

  - Data moved to plotgardenerData package.
  - Default genome assembly updated to "hg38".

BUG FIXES

  - Streamlined parameter parsing and data reading logic.

                      Changes in version 0.0.0.10                       

NEW FEATURES

  - Added unit tests with testthat.
  - bb_annoDomains function addition.
  - bb_plotSignal vertical orientation.

                       Changes in version 0.0.0.9                       

NEW FEATURES

  - Added a NEWS file to track changes to the package.

BUG FIXES

  - Updated viewport parsing for package grid version 4.1.0.