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