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Get STRING Network Image

Source: R/stringdb.R
rba_string_network_image.Rd

This function retrieves a static image of the interaction network among your input proteins and, where applicable, additional interactors. The available arguments control the network contents and appearance.

Usage

rba_string_network_image(
  ids,
  image_format = "image",
  save_image = TRUE,
  species = NULL,
  add_color_nodes = NULL,
  add_white_nodes = NULL,
  required_score = NULL,
  network_flavor = "evidence",
  network_type = "functional",
  hide_node_labels = FALSE,
  use_query_labels = FALSE,
  hide_disconnected_nodes = FALSE,
  hide_structure_pics = FALSE,
  flat_nodes = FALSE,
  node_labels_center = FALSE,
  node_labels_font_size = 12,
  network_term_id = NULL,
  ...
)

Arguments

ids

Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information.
Alternatively, you can retrieve the network of proteins annotated with a STRING functional term by setting ids = NULL and supplying network_term_id.

image_format

Character: 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.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. Required when using network_term_id; otherwise recommended, but required if your input contains more than 10 unique IDs.

add_color_nodes

Numeric: The number of colored nodes (queried proteins and first shell of interactors) to be added.

add_white_nodes

Numeric: The number of white nodes (second shell of interactors) to be added after colored nodes.

required_score

Numeric (between 0 and 1000): Minimum interaction score required for an interaction to be included in the image. If omitted, STRING applies a network-dependent threshold. Common confidence thresholds are 150 (low), 400 (medium), 700 (high), and 900 (highest).

network_flavor

Character: The network-edge style. One of:

  • "evidence": (default) Edge colors indicate the types of evidence supporting each interaction.

  • "confidence": Edge thickness indicates the interaction confidence score.

  • "actions": Edge shape indicates the predicted mode of action.

network_type

Character: One of:

  • "functional": (default) Edges indicate both physical and functional associations.

  • "physical": Edges indicate that two proteins have a physical interaction or are parts of a complex.

hide_node_labels

Logical: (default = FALSE) Hide protein names from the image.

use_query_labels

Logical: (default = FALSE) Use the names supplied in ids as node labels instead of STRING's default labels.

hide_disconnected_nodes

Logical: (default = FALSE) Hide proteins that are not connected to any other protein.

hide_structure_pics

Logical: (default = FALSE) Hide protein structure images inside the nodes.

flat_nodes

Logical: (default = FALSE) Use a flat node design instead of the default 3D design.

node_labels_center

Logical: (default = FALSE) Center protein labels on the nodes.

node_labels_font_size

Numeric (between 5 and 50; default = 12): Font size of the protein node labels.

network_term_id

Character: A functional term identifier (e.g. a Gene Ontology, KEGG, or Reactome identifier). Instead of using proteins supplied through ids, STRING constructs the network from proteins annotated with the specified term. Set ids = NULL and supply species.

...

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

Value

A PNG image array or raw SVG content, depending on image_format.

Corresponding API Resources

"POST https://string-db.org/api/{output-format}/network?identifiers= {your_identifiers}&{optional_parameters}"
"POST https://string-db.org/api/{output-format}/network?network_term_id= {your_term}&{optional_parameters}"

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_interactions_network, rba_string_interaction_partners, rba_string_enrichment_ppi

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

Examples

if (FALSE) { # \dontrun{
rba_string_network_image(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    network_type = "functional",
    save_image = FALSE)
} # }
if (FALSE) { # \dontrun{
rba_string_network_image(ids = c("TP53", "TNF", "EGFR"),
    species = 9606,
    save_image = TRUE)
} # }
if (FALSE) { # \dontrun{
rba_string_network_image(ids = "9606.ENSP00000269305",
    image_format = "highres_image",
    save_image = file.path(getwd(), "TP53_network.png"))
} # }
if (FALSE) { # \dontrun{
rba_string_network_image(
    ids = NULL,
    network_term_id = "GO:0050852",
    species = 9606,
    save_image = FALSE
)
} # }