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ggcoverage 1.4.0

Major changes

  • removed 11 strict dependencies, refactored many functions to work with basic solutions
  • formatted all R code with 'styler'
  • improved arrow style for genomic features

Minor changes

  • fixed overlapping gene arrows issue
  • dont run failing ideogram example check
  • fixed unavailable URLS
  • use tidy description

ggcoverage 1.3.0

Major changes

  • Refactored LoadTrack function.
  • Added GH actions workflow to run automatic R CMD CHECK

Minor changes

  • Handle binning for bam files regardless if done via bamCoverage or GenomicAlignments.
  • Various small linting fixes.
  • Refactored ggcoverage.Rmd and README.Rmd in order to remove all lint errors, adhere to R code style

ggcoverage 1.2.0

Major changes

  • Support protein coverage and annotation plot (ggprotein, geom_protein, geom_feature).

Minor changes

  • Export all themes to simplify customization.
  • Optimized the gene and transcript group.
  • Fix all zero tracks.

ggcoverage 1.1.0

Major changes

  • Mark SNV with twill (add twill to position with SNV), star (add star mark to position with SNV), and highlight (position without SNV is grey).
  • Move FormatTrack to LoadTrackFile, this can reduce load time and memory for big files.
  • Support parallel to handle multiple files more efficiently.

Minor changes

  • geom_coverage and ggcoverage supports changing shared type of y-axis scales across facets (with facet.y.scale parameter).
  • geom_coverage and ggcoverage supports joint view of multiple tracks (with plot.type parameter).
  • geom_coverage and ggcoverage supports joint view of average coverage of multiple tracks (with joint.avg parameter).
  • LoadTrackFile loads bam directly instead of converting bam to bigwig and loading the bigwig.

ggcoverage 1.0.0

Major changes

  • Support Hi-C visualization (geom_tad and geom_tad2).
  • Support genome region interaction visualization (geom_link).
  • Support CNV visualization (geom_cnv).

Minor changes

  • geom_ideogram supports the highlight of centromere.

ggcoverage 0.9.0

Major changes

  • Support gtf file from Ensembl

Minor changes

  • Fixed bugs in getting gene group.

ggcoverage 0.8.1

Minor changes

  • Fixed bugs in ggcoverage.

ggcoverage 0.8.0

Major changes

  • Changed the plot type of coverage when visualizing at single-nucleotide level (geom_bar instead of geom_rect)
  • Changed the plot type of amino acids (geom_rect instead of geom_tile)
  • Changed x axis range
  • Added GetPlotData to obtain raw plot data
  • Added a new vignette to customize the plot

Minor changes

  • Fixed bugs in geom_base.

ggcoverage 0.7.2

New features

  • Added GetConsensusPeak to get consensus peak from replicates with MSPC.

Minor changes

  • Added peak.df for geom_peak to support dataframe as input.

ggcoverage 0.7.0

New features

  • Added geom_base to annotate genome coverage with base and amino acids.

Minor changes

  • LoadTrackFile supported visualization at single-nucleotide level.
  • Added rect.color for geom_coverage to control rect border color.
  • Fixed bug in track file format identification.

ggcoverage 0.6.0

New features

  • Added geom_gc to annotate genome coverage with GC content.

ggcoverage 0.5.0

Minor changes

  • Fixed bug in getIdeogram.

ggcoverage 0.4.0

New features

  • Added geom_peak to enhance its usage in ChIP-seq or ATAC-seq data.
  • Changed Y axis theme.

ggcoverage 0.3.0

New features

  • Added geom_transcript, geom_ideogram.

Minor changes

  • Fixed bug in GetGeneGroup.

ggcoverage 0.2.0

New features

  • Added geom_gene, geom_ideogram.

ggcoverage 0.1.0

New features

  • Added a NEWS.md file to track changes to the package.
  • Added ggcoverage, geom_coverage, LoadTrack and FormatInput.