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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.