v0.3.4

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().

v0.3.2

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().

v0.3.1

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

v0.3.0

• Allow index_snp to be a vector to highlight more than 1 SNP per region.
• 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.

v0.2.1

• 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.

v0.2.0

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.

v0.1.1

Initial release to CRAN