The example data | A basic volcano plot | Highlighting genes of interest | Labelling the top genes automatically | Calling significance on the FDR (or the raw p-value) | Scaling point size | Adding a gene table | Works with DESeq2, edgeR, and limma | Colors and colorblind-safe palettes | Counts, gene sets, and several contrasts | An interactive volcano
Package: ggvolc 0.4.0
ggvolc: Create Volcano Plots for Differential Gene Expression Data
Creates customizable volcano plots for differential gene expression results from RNA-seq analyses. Accepts result objects or tables from 'DESeq2', 'edgeR', and 'limma' directly, with automatic column detection. Labels the most significant or chosen genes, colors gene sets, compares several contrasts side by side, offers colorblind-safe color presets, and can produce interactive plots with 'ggiraph'. Gene tables are rendered with 'gt' and composed with 'patchwork'.
Authors:
ggvolc_0.4.0.tar.gz
ggvolc_0.4.0.zip(r-4.7-any)ggvolc_0.4.0.zip(r-4.6-any)ggvolc_0.4.0.zip(r-4.5-any)
ggvolc_0.4.0.tgz(r-4.6-any)ggvolc_0.4.0.tgz(r-4.5-any)
ggvolc_0.4.0.tar.gz(r-4.7-any)ggvolc_0.4.0.tar.gz(r-4.6-any)
ggvolc_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ggvolc/json (API)
| # Install 'ggvolc' in R: |
| install.packages('ggvolc', repos = c('https://loukesio.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/loukesio/ggvolc/issues
Pkgdown/docs site:https://loukesio.github.io
Datasets:
- all_genes - Gene Expression Analysis Dataset
- attention_genes - Attention Genes Dataset
- edger_genes - EdgeR-style Differential Expression Dataset
- stress_timecourse - Fission Yeast Stress Time Course
bioinformaticsdata-visualizationdeseq2differential-expressiongenomicsggplot2rna-seqvolcano-plot
Last updated from:83661926b5. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 190 | ||
| source / vignettes | OK | 243 | ||
| linux-release | OK | 175 | ||
| macos-release | OK | 144 | ||
| macos-oldrel | OK | 143 | ||
| windows-devel | OK | 135 | ||
| windows-release | OK | 154 | ||
| windows-oldrel | OK | 137 | ||
| wasm-release | OK | 139 |
Exports:de_tablegenes_tableggvolcggvolc_palettes
Dependencies:base64encbigDbitopsbslibcachemclicommonmarkcpp11curldigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2ggrepelggtextgluegridtextgtgtablehighrhtmltoolshtmlwidgetsisobandjpegjquerylibjsonlitejuicyjuiceknitrlabelinglifecyclelitedownmagrittrmarkdownmemoisemimepatchworkpillarpkgconfigpngR6rappdirsRColorBrewerRcppreactablereactRrlangrmarkdownS7sassscalesstringistringrtibbletidyselecttinytexutf8V8vctrsviridisLitewithrxfunxml2yaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene Expression Analysis Dataset | all_genes |
| Attention Genes Dataset | attention_genes |
| Turn a DE result object into a plain data frame | de_table |
| edgeR-style Differential Expression Dataset | edger_genes |
| Combine a Volcano Plot with a gt Table of Genes | genes_table |
| Create a Volcano Plot | ggvolc |
| Color presets for volcano plots | ggvolc_palettes |
| Fission Yeast Stress Time Course (three contrasts) | stress_timecourse |