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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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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