Add Bio Tooltips to HTML Reports

Provides lightweight helpers for adding gene and chemical tooltips to 'R Markdown', 'Quarto', 'shiny', 'pkgdown', and other HTML outputs. The package emits small HTML spans with module-specific data attributes and attaches the browser-side 'bio-tooltips' JavaScript and CSS assets through 'htmltools'. Entity lookup and rendering are handled in the browser by 'bio-tooltips'; this package does not query biological databases from R during package checks.

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")

Documentation

• CRAN package page, vignette, and reference manual
• GitHub repository

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 2.3.2, 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 = "2.3.2")