Get STRING Network Image

Depending on that you supplied a single protein ID or more than one protein ID, this function will produce a static image of the interaction networks among your input proteins or/and with other proteins. See the "Arguments" section to learn more about how you can modify the network image.

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 = "confidence",
  network_type = "functional",
  hide_node_labels = FALSE,
  hide_disconnected_nodes = FALSE,
  hide_structure_pics = FALSE,
  ...
)

Arguments

ids

Your protein ID(s). It is strongly recommended to supply STRING IDs. See rba_string_map_ids for more information.

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.

species

Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. (Recommended, but optional if your input is less than 100 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: A minimum of interaction score for an interaction to be included in the image. if not supplied, the threshold will be applied by STRING Based in the network. (low Confidence = 150, Medium Confidence = 400, High Confidence = 700, Highest confidence = 900)

network_flavor

The style of network edges, should be one of:

"confidence": (default) Line's thickness is an indicator of the interaction's confidence score.
"evidence": Line's color is based on the type of evidences that support the interaction.
"action": Line's Shape is an indicator of the interaction's predicted mode of actions.

network_type

should be one of:

"functional": (default) The edge's indicate both physical and functional associations.
"physical": The edges indicate that two proteins have a physical interaction or are parts of a complex.

hide_node_labels

Logical: (Default = FALSE) Hide proteins names from the image?

hide_disconnected_nodes

Logical: (Default = FALSE) Hide proteins that are not connected to any other proteins from the image?

hide_structure_pics

Logical: (Default = FALSE) Hide protein's structure picture from inside the bubbles?

...

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

Value

A network images which can be PNG or SVG depending on the inputs.

Corresponding API Resources

"POST https://string-db.org/api/[output-format]/network?identifiers= [your_identifiers]&[optional_parameters]"

References

Damian Szklarczyk, Annika L Gable, Katerina C Nastou, David Lyon, Rebecca Kirsch, Sampo Pyysalo, Nadezhda T Doncheva, Marc Legeay, Tao Fang, Peer Bork, Lars J Jensen, Christian von Mering, The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D605–D612, https://doi.org/10.1093/nar/gkaa1074
STRING API Documentation
Citations note on STRING website

Examples

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