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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()
.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()
.data
and gene
arguments in locus()
since most users specify the data
object first.ylim
issue affecting secondary y axis with
recombination line.gg_scatter()
.eqtl_plot()
with locus plots with
recombination rate.gg_scatter()
.gg_scatter()
.link_LD()
(only works with LDproxy
method).locus()
.locus()
.scatter_plotly()
.index_snp
to be a vector to highlight more than 1
SNP per region (suggested by Luke Pilling).LDproxy
in
link_LD()
. This is now the default option.locus_plot()
, locus_ggplot()
,
genetracks()
and gg_genetracks()
.link_recomb()
, which is much faster when plotting
multiple loci.locus_ggplot()
and
gg_scatter()
(thanks to Tom Willis).link_recomb()
locus_plot()
and
locus_ggplot()
.scatter_plot()
arguments chromCol
and
sigCol
are replaced by scheme
which now allows
setting of the index SNP colour.gg_genetracks()
to enable easy layering of several ggplot2
plots above a row of gene tracks (thanks to nickhir for the
suggestion).data
(or setting it
to NULL
) when calling locus()
.quick_peak()
for quickly finding peaks
in GWAS datasets.link_recomb()
for retrieving
recombination data from UCSC.locus_plot()
and locus_ggplot()
....
to link_LD()
and
link_eqtl()
to allow passing of additional arguments such
as genome_build
to LDlinkR
queries.LDtoken
in link_LD()
and
link_eqtl()
has been renamed token
to be
consistent with LDlinkR
.locus_ggplot()
and locus_plotly()
.locus_plotly()
yzero
argument in scatter plotsThese 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.