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.
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.
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()