Changes in version 2.6.0                        

  - Added preliminary modbam file support.
  - Changed rug plot to appear under other geoms. This helps with
    visibility of data when methylation values are close to 0.
  - Changed heatmap alpha from 0.5 to 1, line width from 1.0 to 1.2 and
    line colour from black to darkgrey.
  - Changed x-axis limits on plots to be controlled using
    coord_cartesian instead of scale_x_continuous. Plots should now
    accurately represent data around the boundaries.

                        Changes in version 2.4.0                        

  - Fixed plot_region_heatmap() producing the wrong plot when a factor
    is used for the chromosome.
  - Fixed nanopolish and f5c import positions being off by 1.
  - Fixed broken samples() setter for NanoMethResults.
  - Added plot_agg_genes() function as a shorthand for
    plot_agg_regions(x, exons_to_genes(exons(x))).
  - Added the ability to interrupt methy_to_bsseq() calls.
  - Added handling for NanoMethResults objects in filter_methy(). If
    NanoMethResult is used as input, then NanoMethResult is invisibly
    returned as output.
  - Added black outlines to exons in annotation to distinguish
    contiguous segments for features like tandem repeats.
  - Added line_size argument to plot_gene(), plot_region() and
    plot_granges() plots for adjusting line size.
  - Added subsample argument to heatmap plots, default 50. This reduces
    the number of rows shown the plot to the specified amount.
  - Added get_exons_mm10(), get_exons_hg19(), and get_exons_hg38() as
    replacements for get_exons_mus_musculus() and
    get_exons_homo_sapiens().
  - Changed heatmaps to no longer plot samples that are absent from
    sample annotations.
  - Changed heatmap labels to appear on the right rather than on top.
  - Changed heatmap alpha from 0.33 to 0.5.
  - Changed arrows in exon connectors to appear in the middle as open
    arrow instead of at the end as closed arrow.
  - Changed default X axis labels to be rescaled to appropriate
    SI-style. e.g. Kb, Mb, Gb.

                        Changes in version 2.2.0                        

  - Added heatmap argument to plot_gene(), plot_region() and
    plot_granges(). This adds a read-heatmap to the plot.
  - Added cluster_regions() function to perform k-means clustering on a
    table of genomic regions based on methylation profile.
  - Added median averaging method for trends in plot_gene(),
    plot_region() and plot_granges(). This can be changed using the new
    avg_method argument, default is mean.
  - Added filter_methy() function to create a filtered methylation file.
  - Added region_methy_stats() to obtain average methylation fractions
    of specific regions.
  - Added methy_to_edger() direct conversion wrapper around
    methy_to_bsseq() and bsseq_to_edger().
  - Added palette argument to plot_gene(), plot_region() and
    plot_granges() to allow custom colour palettes.
  - Fixed bsseq_to_edger() failing when regions argument was used.
  - Fixed heatmaps not staying in a single column when more than 2
    groups were present.

                        Changes in version 2.0.0                        

  - Major changes to plot_agg_regions().
      - Features of plot_agg_regions() and
        plot_agg_regions_sample_grouped() merged into one interface.
      - Regions now specified using single table.
  - Changed plot_regions() default window proportion to 0.
  - Changed default theme from theme_bw() to theme_tufte().
  - Added Megalodon data import instructions to "Importing Data"
    vignette.
  - Added scico palette defaults for heatmaps. These are colourblind
    friendly.
  - Added check for 0 length queries which would cause program to hang
    indefinitely.
  - Added setters for NanoMethResult attributes methy, samples and
    exons.
  - Added MDS and PCA plots.
  - Added vignette for using external annotation and dimensionality
    reduction.
  - Added binary thresholding for plot_gene(), plot_region() and
    plot_agg_regions().
  - Added regions argument to bsseq_to_edger() to calculate aggregate
    counts over features rather than per site.

                        Changes in version 1.1.4                        

  - Added palette argument to aggregate plots
  - Added exons_to_genes() function to convert exon annotation to gene
    annotation
  - Added plot_granges_heatmap() function to use GRanges for plotting
    heatmaps

                        Changes in version 1.1.3                        

  - Fixed group handling for list region input in plot_agg_regions()
  - Fixed unused window size argument in plot_region_heatmap()
  - Fixed error when reads overlap in name and position for internal
    function StatLM()

                        Changes in version 1.1.2                        

  - Changed example dataset exon annotations from all genomic exons to
    just those contained in data.
  - Fixed methylation heatmap to no longer be hard coded for Peg3.
  - Added plot_region_heatmap() as analogue to plot_region().
  - Fixed plot_agg_regions_sample_grouped() to use group column of
    NanoMethViz::samples(x) rather than haplotype.
  - Added unit tests.

                        Changes in version 1.1.1                        

  - Added methylation heatmap via plot_gene_heatmap().
  - Fixed gene_anno() in plot_gene() for argument so FALSE actually
    turns off gene annotation.
  - Added warning for cpp11 versions <0.2.5 which may cause memory
    crashes when trying to import methylation data.
  - Added cpp11 version dependency to address tidyverse/readr#1145.
  - Added query methylation by gene using query_methy_gene().

                        Changes in version 1.0.0                        

  - Initial Bioconductor release.