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NEWS.md

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News

locuszoomr 0.3.5

15/09/2024
  • Fixed vignette issues causing CRAN check errors.

locuszoomr 0.3.4

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().

locuszoomr 0.3.2

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().

locuszoomr 0.3.1

28/06/2024
  • Add toggle for using webGL in scatter_plotly().
  • Add height control in plotly functions.

locuszoomr 0.3.0

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.

locuszoomr 0.2.1

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.

locuszoomr 0.2.0

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.

locuszoomr 0.1.3

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

locuszoomr 0.1.2

02/11/2023
  • This is the initial build of locuszoomr