Changes in version 0.3.9                        

27/03/2026

  - Added prioritise argument to allow users to place important genes
    first in the gene tracks.
  - Protein-coding genes are prioritised in the gene tracks.

                 Changes in version 0.3.8 (2025-03-03)                  

26/02/2025

  - Fixed handling of tibbles.

                 Changes in version 0.3.7 (2025-02-10)                  

05/02/2025

New features

  - Added recomb_offset argument to enable y offset to shift scatter
    points up slightly away from the recombination line to reduce the
    overlap. Works with both locus_plot() and locus_ggplot().
  - Added ylim and ylim2 arguments to scatter_plot() and gg_scatter() to
    make it easier to set y axis and secondary y axis (recombination
    line) limits in locus_plot() and locus_ggplot().

Important change

  - Changed the order of data and gene arguments in locus() since most
    users specify the data object first.

Fixes

  - Fixed ylim issue affecting secondary y axis with recombination line.

                 Changes in version 0.3.6 (2025-01-25)                  

09/01/2025

  - Add option to show gene names in italics.
  - Added citation.

                 Changes in version 0.3.5 (2024-09-15)                  

15/09/2024

  - Fixed vignette issues causing CRAN check errors.

                 Changes in version 0.3.4 (2024-09-06)                  

06/09/2024

New features

  - Added full support for point shapes in gg_scatter().

Fixes

  - Fix for alignment of eqtl_plot() with locus plots with recombination
    rate.
  - Bugfix for recombination rate axis title font size.
  - Bugfix beta symbols in gg_scatter().
  - Fixes to legends in gg_scatter().

                 Changes in version 0.3.2 (2024-08-19)                  

18/08/2024

  - Fix for SNPs with chromosome coordinate format in link_LD() (only
    works with LDproxy method).
  - Fix for non-human ensembl databases e.g. mouse in locus().
  - Record ensembl version, organism and genome in locus objects.
  - Bugfix: give an error message if gene is not found in ensembl
    database in locus().

                 Changes in version 0.3.1 (2024-07-03)                  

28/06/2024

  - Add toggle for using webGL in scatter_plotly().
  - Add height control in plotly functions.

                 Changes in version 0.3.0 (2024-04-16)                  

16/04/2024

  - Allow index_snp to be a vector to highlight more than 1 SNP per
    region (suggested by Luke Pilling).
  - Altered default colour scheme.
  - Multiple improvements to plotly version.
  - Added option to use the much faster LDproxy in link_LD(). This is
    now the default option.
  - Added support for plotting loci with eQTL data to show multiple
    genes in different colours.
  - Added ability to overlay up/down pointing triangles to show sign of
    beta coefficient for significant SNPs.
  - Added highlighting of selected genes with individual colours in the
    gene tracks in locus_plot(), locus_ggplot(), genetracks() and
    gg_genetracks().
  - Enable use of downloadable recombination rate track files from UCSC
    in link_recomb(), which is much faster when plotting multiple loci.

                 Changes in version 0.2.1 (2024-02-17)                  

17/02/2024

  - Added labels to locus_ggplot() and gg_scatter() (thanks to Tom
    Willis).
  - Improved error handling in link_recomb()
  - Ensure index SNP is plotted on top in locus_plot() and
    locus_ggplot().
  - In scatter_plot() arguments chromCol and sigCol are replaced by
    scheme which now allows setting of the index SNP colour.

                 Changes in version 0.2.0 (2024-01-08)                  

21/12/2023

New features

  - Improved ggplot2 gene track plotting via gg_genetracks() to enable
    easy layering of several ggplot2 plots above a row of gene tracks
    (thanks to nickhir for the suggestion).
  - For those that only want the gene tracks for their own plots, this
    is now easier by simply not specifying data (or setting it to NULL)
    when calling locus().
  - Added function quick_peak() for quickly finding peaks in GWAS
    datasets.
  - Added function link_recomb() for retrieving recombination data from
    UCSC.
  - Recombination rate is shown on a secondary y axis by locus_plot()
    and locus_ggplot().
  - Added ... to link_LD() and link_eqtl() to allow passing of
    additional arguments such as genome_build to LDlinkR queries.

Changes

  - Argument LDtoken in link_LD() and link_eqtl() has been renamed token
    to be consistent with LDlinkR.

Bugfixes

  - Fixed bug when plotting LD with absent levels in locus_ggplot() and
    locus_plotly().
  - Fixed plots with no gene tracks (thanks to Tom Willis).
  - Genes with missing gene symbols now display the ensembl gene ID.

                 Changes in version 0.1.3 (2023-12-06)                  

03/11/2023

  - Added arrows to the gene tracks in locus_plotly()
  - Fixed bug relating yzero argument in scatter plots
  - Improved labelling
  - Fixed CRAN ERROR relating to package EnsDb.Hsapiens.v75 in Suggests

                 Changes in version 0.1.2 (2023-11-02)                  

02/11/2023

  - This is the initial build of locuszoomr