News
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