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Get STRING Enrichment Plot

Source: R/stringdb.R
rba_string_enrichment_image.Rd

In addition to performing enrichment analysis, STRING allows you to also visualize the analysis results. Use rba_string_enrichment to retrieve the analysis results as a data frame.

Usage

rba_string_enrichment_image(
  ids,
  species,
  category = "Process",
  image_format = "image",
  save_image = TRUE,
  group_by_similarity = NULL,
  color_palette = "mint_blue",
  number_of_term_shown = 10,
  x_axis = "signal",
  ...
)

Arguments

ids

Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information. Note that if only one id is supplied, STRING expands the network by 10 proteins.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606.

category

The terms set to use to perform enrichment analysis. valid values are (See details for more info): "Process" (default), "Function", "Component", "Keyword", "KEGG", "RCTM", "HPO", "MPO", "DPO", "WPO", "ZPO", "FYPO", "Pfam", "SMART", "InterPro", "PMID", "NetworkNeighborAL", "COMPARTMENTS", "TISSUES", "DISEASES", or "WikiPathways"

image_format

one of:

  • "image": PNG image with normal resolution.

  • "highres_image": High-resolution PNG image.

  • "svg": Scalable Vector Graphics image.

save_image

Logical or Character:

  • TRUE: Save the image to an automatically-generated path.

  • FALSE: Do not save the image, just return it as an R object.

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

group_by_similarity

Jackard index treshold to visually group the related terms. Valid values are between 0.1 to 1 with increment of 0.1. Default value is NULL (i.e. no grouping).

color_palette

Color pallet to code FDR values. Valid values are: "mint_blue" (default), "lime_emerald", "green_blue", "peach_purple", "straw_navy", or "yellow_pink"

number_of_term_shown

(default: 10) Maximum number of results to include in the plot.

x_axis

The variable to show on the x axis and rank the results based on it. Valid values are: "signal" (default), "strength", "FDR", or "gene_count"

...

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

Value

A plot summarizing the enrichment results, which can be PNG or SVG depending on the inputs.

Details

Available values for category are as follow. Default value is "Process".

  • Process: Biological Process (Gene Ontology)

  • Function: Molecular Function (Gene Ontology)

  • Component: Cellular Component (Gene Ontology)

  • Keyword: Annotated Keywords (UniProt)

  • KEGG: KEGG Pathways

  • RCTM: Reactome Pathways

  • HPO: Human Phenotype (Monarch)

  • MPO: The Mammalian Phenotype Ontology (Monarch)

  • DPO: Drosophila Phenotype (Monarch)

  • WPO: C. elegans Phenotype Ontology (Monarch)

  • ZPO: Zebrafish Phenotype Ontology (Monarch)

  • FYPO: Fission Yeast Phenotype Ontology (Monarch)

  • Pfam: Protein Domains (Pfam)

  • SMART: Protein Domains (SMART)

  • InterPro: Protein Domains and Features (InterPro)

  • PMID: Reference Publications (PubMed)

  • NetworkNeighborAL: Local Network Cluster (STRING)

  • COMPARTMENTS: Subcellular Localization (COMPARTMENTS)

  • TISSUES: Tissue Expression (TISSUES)

  • DISEASES: Disease-gene Associations (DISEASES)

  • WikiPathways: WikiPathways

Corresponding API Resources

"POST https://string-db.org/api/{output_format}/enrichmentfigure"

References

  • Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L Gable, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D638–D646, https://doi.org/10.1093/nar/gkac1000

  • STRING API Documentation

  • Citations note on STRING website

See also

rba_string_map_ids, rba_string_enrichment, rba_string_annotations

Other "STRING": rba_string_annotations(), rba_string_enrichment(), rba_string_enrichment_ppi(), rba_string_homology_inter(), rba_string_homology_intra(), rba_string_interaction_partners(), rba_string_interactions_network(), rba_string_map_ids(), rba_string_network_image(), rba_string_version()

Other "Enrichment/Over-representation": rba_enrichr(), rba_mieaa_enrich(), rba_panther_enrich(), rba_reactome_analysis(), rba_string_enrichment()

Examples

if (FALSE) { # \dontrun{
  rba_string_enrichment(
  ids = c("TP53", "TNF", "EGFR"),
  species = 9606)
} # }
if (FALSE) { # \dontrun{
  rba_string_enrichment(
  ids = c("TP53", "TNF", "EGFR"),
  species = 9606,
  category = "KEGG")
} # }
if (FALSE) { # \dontrun{
  rba_string_enrichment(
  ids = c("TP53", "TNF", "EGFR"),
  species = 9606,
  x_axis = "strength",
  number_of_term_shown = 20
  )
} # }
if (FALSE) { # \dontrun{
  rba_string_enrichment(
  ids = c("TP53", "TNF", "EGFR"),
  species = 9606,
  color_palette = "straw_navy"
  )
} # }