NEWS.md

In locuszoomr: Gene Locus Plot with Gene Annotations

News

locuszoomr 0.3.8

26/02/2025

• Fixed handling of tibbles.

locuszoomr 0.3.7

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.

locuszoomr 0.3.6

09/01/2025

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

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

locuszoomr documentation built on April 12, 2025, 2:28 a.m.