Overview | Installation | Loading variant data | Option 1: From a VCF file | Option 2: From a data frame or Excel export | Lollipop plot | Adding protein domain annotations | Colouring by sample | Customising further | Consequence summary | By sample | Proportional view | By gene | Mutational spectrum | Faceted by sample | Interactive plots | Colour palettes and theming | Access the built-in palettes | Apply the theme to your own plots | Summary | Session information
Package: ggvariant 0.2.0
ggvariant: Tidy, 'ggplot2'-Native Visualization for Genomic Variants
A simple, opinionated toolkit for visualizing genomic variant data using a 'ggplot2'-native grammar. Accepts VCF files or plain data frames and produces lollipop plots, consequence summaries, mutational spectrum charts, and cohort-level comparisons as standard 'ggplot2' objects. Designed for both wet-lab biologists and experienced bioinformaticians.
Authors:
ggvariant_0.2.0.tar.gz
ggvariant_0.2.0.zip(r-4.7-any)ggvariant_0.2.0.zip(r-4.6-any)ggvariant_0.2.0.zip(r-4.5-any)
ggvariant_0.2.0.tgz(r-4.6-any)ggvariant_0.2.0.tgz(r-4.5-any)
ggvariant_0.2.0.tar.gz(r-4.7-any)ggvariant_0.2.0.tar.gz(r-4.6-any)
ggvariant_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggvariant/json (API)
| # Install 'ggvariant' in R: |
| install.packages('ggvariant', repos = c('https://josh45-source.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/josh45-source/ggvariant/issues
Pkgdown/docs site:https://josh45-source.github.io
genomicsggplot2variant-visualizationvcf
Last updated from:e45f66c2cf. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 154 | ||
| source / vignettes | OK | 206 | ||
| linux-release | OK | 205 | ||
| macos-release | OK | 190 | ||
| macos-oldrel | OK | 183 | ||
| windows-devel | OK | 117 | ||
| windows-release | OK | 126 | ||
| windows-oldrel | OK | 88 | ||
| wasm-release | OK | 118 |
Exports:coerce_variantsgv_paletteplot_consequence_summaryplot_lollipopplot_oncoprintplot_tmbplot_variant_spectrumplot_waterfallread_vcftheme_ggvariant
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ggvariant: Tidy, ggplot2-Native Visualization for Genomic Variants | ggvariant-package ggvariant |
| Coerce a plain data frame to a 'gvf' object | coerce_variants |
| ggvariant colour palettes | gv_palette |
| Print and summarise 'gvf' objects | gvf-methods print.gvf print.summary.gvf summary.gvf |
| Consequence summary bar chart | plot_consequence_summary |
| Lollipop plot of variants along a gene | plot_lollipop |
| Oncoprint / waterfall plot of variants across samples | plot_oncoprint plot_waterfall |
| Tumour mutational burden bar chart | plot_tmb |
| Mutational spectrum (SBS) bar chart | plot_variant_spectrum |
| Read a VCF file into a tidy variant data frame | read_vcf |
| ggvariant ggplot2 theme | theme_ggvariant |