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Generate PDF file with Reactome Analysis Results

Source: R/reactome_analysis.R
rba_reactome_analysis_pdf.Rd

Use this function to save a detailed report of your previous analysis (That you have done with rba_reactome_analysis). You need to supply a 'token' associated to your previous analysis.

Usage

rba_reactome_analysis_pdf(
  token,
  species,
  save_to = NULL,
  number = 25,
  resource = "TOTAL",
  diagram_profile = "Modern",
  analysis_profile = "Standard",
  fireworks_profile = "Barium Lithium",
  ...
)

Arguments

token

Character: A token associated to your previous Reactome analysis.

species

Character or Numeric: NCBI Taxonomy identifier (Human Taxonomy ID is 9606.) or species name (e.g. "Homo sapiens"). See rba_reactome_species or Reactome Data Schema: Entries: Species.

save_to

NULL or Character: (optional)

  • NULL: Save the file to an automatically-generated path.

  • Character string: A valid file path to save the file to.

number

Numeric: (default = 25) Positive integer giving the maximum number of pathways to include in the report.

resource

Character: (default = "TOTAL") Filter results based on the resource. Available choices are: "TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND" or "PUBCHEM_COMPOUND".

diagram_profile

Character: (default = "Modern") Color profile of diagrams, should be either "Modern" or "Standard".

analysis_profile

Character: (default = "Standard") Color profile of analysis, should be one of: "Standard", "Strosobar" or "Copper Plus".

fireworks_profile

Character: (default = "Barium Lithium") Color profile of the overview diagram, should be one of: "Cooper", "Cooper Plus", "Barium Lithium" or "Calcium Salts".

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Value

NULL, a PDF file will be saved to disk.

Details

Token is associated to each Reactome analysis results and kept by Reactome for at least 7 days. You can locate it in rba_reactome_analysis's output, under a sub-list named "summary" (i.e. results$summary$token).
Note that Reactome will store your token for only 7 days. You can download your full results with rba_reactome_analysis_download, and re-import it anytime to reactome (using rba_reactome_analysis_import) to generate a new token. Use rba_reactome_analysis_download to save your results in other formats.

Corresponding API Resources

"GET https://reactome.org/AnalysisService/report/{token}/{species}/ {filename}.pdf"

References

  • Ragueneau, E., Gong, C., Sinquin, P., Sevilla, C., Beavers, D., Grentner, A., ... D’Eustachio, P. (2026). The Reactome Knowledgebase 2026. Nucleic Acids Res., 54(D1), D673–D681. doi: 10.1093/nar/gkaf1223

  • Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.

  • Reactome Analysis Services API Documentation

  • Citations note on Reactome website

See also

rba_reactome_analysis_download rba_reactome_analysis

Other "Reactome Analysis Service": rba_reactome_analysis(), rba_reactome_analysis_download(), rba_reactome_analysis_import(), rba_reactome_analysis_mapping(), rba_reactome_analysis_species(), rba_reactome_analysis_token()

Examples

if (FALSE) { # \dontrun{
rba_reactome_analysis_pdf(token = "MjAyMDEwMTYwMTI3MTNfMjY1MjM%3D",
    species = 9606, save_to = "my_analysis.pdf")
} # }