BioTooltipR

BioTooltipR is a lightweight R helper package for adding browser-side bio-tooltips gene and chemical tooltips to R Markdown, Quarto, Shiny, pkgdown, and other HTML reports.

The R package does not reimplement the bio-tooltips JavaScript library in R. Instead, it:

1. emits ordinary HTML spans such as <span class="gene-tooltip">TP53</span>;
2. attaches the bio-tooltips JavaScript/CSS bundle through htmltools;
3. makes common R reporting patterns pleasant, especially inline prose and tables.

Installation

Install the released version from CRAN:

install.packages("BioTooltipR")

Minimal R Markdown example

library(BioTooltipR)

use_bio_tooltips()

Then use inline helpers in prose:

The tumour suppressor `r gene_tt("TP53", species = "human")` responds to many forms of cellular stress.

Chemical tooltips can use visible-text lookup or stable identifiers:

chem_tt("aspirin", query = "2244", scope = "pubchem")
chem_tt("caffeine", lookup = "best-guess")

Tables

library(BioTooltipR)

use_bio_tooltips(modules = "gene")

top_genes <- data.frame(
  symbol = c("TP53", "BRCA1", "GADD45A"),
  log2FoldChange = c(2.1, -1.4, 1.2),
  padj = c(0.0004, 0.002, 0.01)
)

top_genes |>
  gene_column(symbol, species = "human") |>
  bt_kable()

bt_kable() uses escape = FALSE by default so tooltip spans render as HTML.

Explicit lower-level markup

gene_tt("Trp53", species = "mouse")
chem_tt("benzo[a]pyrene", query = "2336", scope = "pubchem")

Experimental auto-linking

For already-rendered prose, use a constrained vocabulary rather than scanning blindly:

auto_gene_tooltips(
  genes = c("TP53", "BRCA1", "GADD45A"),
  species = "human",
  selector = ".results-section"
)

This feature is intentionally opt-in because many gene symbols are ordinary English words or ambiguous strings.

Asset strategy

By default, use_bio_tooltips() uses vendored bio-tooltips 1.1.1, D3 7.9.0, and Ideogram 1.53.0 browser assets included with this R package. D3 and Ideogram are loaded only for the gene module. CDN assets remain available when explicitly requested:

use_bio_tooltips(cdn = TRUE, version = "1.1.1")