NEWS
locuszoomr 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.
locuszoomr 0.3.8 (2025-03-03)
26/02/2025
- Fixed handling of tibbles.
locuszoomr 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.
locuszoomr 0.3.6 (2025-01-25)
09/01/2025
- Add option to show gene names in italics.
- Added citation.
locuszoomr 0.3.5 (2024-09-15)
15/09/2024
- Fixed vignette issues causing CRAN check errors.
locuszoomr 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().
locuszoomr 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().
locuszoomr 0.3.1 (2024-07-03)
28/06/2024
- Add toggle for using webGL in
scatter_plotly().
- Add height control in plotly functions.
locuszoomr 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.
locuszoomr 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.
locuszoomr 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.
locuszoomr 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
locuszoomr 0.1.2 (2023-11-02)
02/11/2023
- This is the initial build of locuszoomr