Generate PDF file with Reactome Analysis ResultsSource:
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.
rba_reactome_analysis_pdf( token, species, save_to = NULL, number = 25, resource = "TOTAL", diagram_profile = "Modern", analysis_profile = "Standard", fireworks_profile = "Barium Lithium", ... )
A token associated to your previous Reactome analysis.
NULL or Character:
NULL: Save the file to an automatically-generated path.
Character string: A valid file path to save the file to.
Numeric: Maximum number of the reported pathways. Cannot not be greater than 50.
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".
Color profile of diagrams, should be either "Modern" (default) or "Standard".
Color profile of analysis, should be one of: "Standard" (default), "Strosobar" or "Copper Plus".
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.
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
rba_reactome_analysis_import) to generate
a new token.
rba_reactome_analysis_download to save your results
in other formats.
"GET https://reactome.org/AnalysisService/report/token/species/ filename.pdf"
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.