geneviewer 0.2.0 is on CRAN: interactive gene cluster figures in R

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Hi all,

I'm happy to share that geneviewer 0.2.0 is now on CRAN. geneviewer is an R package for drawing gene clusters, gene arrow maps and transcripts as interactive htmlwidgets. You can use them in the RStudio viewer, R Markdown/Quarto documents and Shiny apps, and export them for publications.

geneviewer: load files, build a chart, zoom in, drag labels, switch themes and save the figure

install.packages("geneviewer")

What it does

  • Reads GenBank, FASTA, GFF and BED files, or works from a plain data frame
  • Compares clusters with protein alignments or MUMmer, and draws the links between them
  • Adds titles, labels, legends, scales, annotations and tooltips, all from R

New in 0.2.0

  • Themes and patterns: GC_theme() gives the whole chart a built-in look (including publication and black & white themes), and GC_pattern() fills genes with patterns for greyscale figures
  • Zooming: GC_zoom() adds a zoom bar for long clusters and genomes
  • Editing in the chart: drag labels, titles, scales and legend items, with undo and redo. Selected positions can be saved back to your R code with GC_element_style()
  • Save as SVG: the whole chart as one vector file, ready for Illustrator, Inkscape or a journal
  • Shiny events: GC_events() reports clicks, selections and zooms to your app
  • Faster and smaller: large clusters draw about 10x faster, and protein_blast() is 3–9x faster

Try it without installing anything: the Gene Cluster Dashboard runs geneviewer in your browser with Shinylive. Load your files, edit the chart by clicking, and copy the R code that recreates it.

Links

I'd love to hear what you build with it, and what's missing.