NEWS

locuszoomr 0.3.7 (2025-02-10)

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().

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

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().

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.

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.

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.

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

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.