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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

A token associated to your previous Reactome analysis.

species

Numeric or Character: 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:

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

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

number

Numeric: Maximum number of the reported pathways. Cannot not be greater than 50.

resource

Filter results based on the resource. Default is "TOTAL", available choices are: "TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND", "ENTITIES_FDR" or "PUBCHEM_COMPOUND".

diagram_profile

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

analysis_profile

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

fireworks_profile

Color profile of overview diagram, should be one of: "Copper", "Copper 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

  • Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028

  • 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")
} # }