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Get a Reactome Pathway Overview

Source: R/reactome_content.R
rba_reactome_exporter_overview.Rd

This function will save a pathway overview of the supplied species as an image file.

Usage

rba_reactome_exporter_overview(
  species,
  output_format = "png",
  save_to = NULL,
  image_quality = 5,
  flag_element = NULL,
  flg_interactors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  diagram_profile = "Copper",
  token = NULL,
  resource = "TOTAL",
  exp_column = NULL,
  coverage = FALSE,
  ...
)

Arguments

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.

output_format

Character: (default = "png") Image format, can be one of: png, jpg, jpeg, svg or gif.

save_to

NULL or Character: (default = NULL)

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

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

image_quality

Numeric: (default = 5) A number ranging from 1 to 10. 1 is the lowest quality and 10 is the highest.

flag_element

Character: (optional) Gene name, protein ID, chemical ID or Reactome ID of a diagram's element to be flagged.

flg_interactors

Logical: (default = TRUE) Should the interactor be considered when flagging a diagram element?

sel

Character vector: (optional) CSV line for highlighting element(s) selection in the diagram.

title

Logical: (default = TRUE) Should the pathway name be displayed below the image?

margin

Numeric: (default = 15) A number ranging from 0 to 20 to set as the image's margin.

diagram_profile

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

token

Character: (optional) The analysis Token for which the results will be overlaid on top of the given pathways overview. see: rba_reactome_analysis.

resource

Character: (default = "TOTAL") The analysis resource for which the results will be overlaid on top of the given pathways overview.

exp_column

Numeric: (optional) (only if token is supplied) Specify the expression column for the overlay.

coverage

Logical: (default = FALSE) Should the analysis coverage values be overlaid?

...

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

Value

NULL, Based to the inputs, an image file will be saved to disk.

Corresponding API Resources

"GET https://reactome.org/ContentService/exporter/fireworks/{species}.{ext}"

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. (2020). ReactomeGSA—Efficient Multi-Omics Comparative Pathway Analysis. Molecular & Cellular Proteomics, 19(12), 2115–2125. doi: 10.1074/mcp.TIR120.002155

  • Reactome Content Services API Documentation

  • Citations note on Reactome website

See also

rba_reactome_analysis

Other "Reactome Content Service - Format Exporter": rba_reactome_exporter_diagram(), rba_reactome_exporter_event(), rba_reactome_exporter_reaction()

Examples

if (FALSE) { # \dontrun{
rba_reactome_exporter_overview(species = 9606,
    output_format = "svg",
    save_to = "human_pathways.svg")
} # }
if (FALSE) { # \dontrun{
rba_reactome_exporter_overview(species = 9606,
    token = 123456789)
} # }