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plot_oncoprint() / plot_waterfall():
a gene-by-sample mutation matrix (the same visualisation under the
ComplexHeatmap/cBioPortal and
GenVisR/maftools community names,
respectively). Genes are ranked by descending number of altered samples;
samples are ordered by the memo-sort/cascade algorithm for the
characteristic staircase pattern. Multi-hit cells (a gene mutated more
than once in one sample) render as a distinct "Multi_Hit"
category. Supports an optional clinical annotation track from a
sample-metadata data frame. Suggested by Nour-al-dain Marzouka
(#N).plot_tmb(): a per-sample tumour mutational burden
bar chart, raw counts or normalised to mutations/Mb.read_vcf()’s gvf objects now have real
print.gvf() and summary.gvf() methods, showing
a compact header and consequence/ sample/chromosome breakdowns instead
of a raw data.frame dump.read_vcf() no longer attaches a variant to a
homozygous-reference ("0/0") sample.
.pivot_samples()’s presence check only excluded literal
missing-genotype codes, so every sample was pivoted in as carrying every
variant regardless of its actual genotype on any multi-sample VCF. This
affected every per-sample dimension of read_vcf()’s output:
plot_lollipop(color_by = "sample"),
plot_consequence_summary()’s per-sample bars, and both new
sample-aware plots above. Predates this release entirely (present since
0.1.0) (#3).plot_variant_spectrum()’s
context/genome arguments and
read_vcf()’s info_fields argument now abort
with an informative error instead of being silently ignored. None of the
three were actually implemented, despite being documented (#1, #2).#CHROM header line, or containing a
data line with the wrong number of tab-separated fields, now aborts with
a clear message instead of failing deep inside on an opaque base-R
error.normalizePath()’s base-R error.read_vcf()’s .parse_ann_csq() (ANN/CSQ
INFO field parsing) is now vectorised over the whole INFO column instead
of looping row by row. ~8.75x faster in isolation on a synthetic
100,000-record VCF (8.05s -> 0.92s); full read_vcf() on
the same file drops from 11.62s to 3.68s.ggvariant.Rmd to activate the “Get started” navbar
convention, and three new articles (Gallery, interactive plots,
customising with ggplot2) live in vignettes/articles/
rather than the shipped vignettes, per R Packages’ guidance for
graphics-heavy content.Mutation 1.pdf,
Rplot*.png/.pdf, etc.) that were shipping
inside the package tarball and triggering an R CMD check
WARNING and NOTE.R-CMD-check, test-coverage, and
pkgdown GitHub Actions workflows, and fixed the Codecov
badge, which pointed at a nonexistent main branch.vdiffr
visual regression snapshots.read_vcf() and coerce_variants() read VCF
files or plain data frames into a tidy gvf object.plot_lollipop(),
plot_consequence_summary(), and
plot_variant_spectrum() provide ggplot2-native
variant visualizations.gv_palette() and theme_ggvariant() provide
built-in colour palettes and a shared plot theme.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.
Health stats visible at Monitor.