rbioapi: rba_string_network_image – R documentation

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rba_string_network_image

Get STRING Network Image

Description

Depending on that you provided 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. Refer to 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 = NA,
  add_color_nodes = NA,
  add_white_nodes = NA,
  required_score = NA,
  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 provide 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 provided, 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). Refer to `rba_options`'s arguments documentation 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

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613. doi: 10.1093/nar/gky1131. PMID: 30476243; PMCID: PMC6323986.
STRING API Documentation

Examples

## Not run: 
rba_string_network_image(ids = c("9606.ENSP00000269305",
    "9606.ENSP00000398698",
    "9606.ENSP00000275493"),
    network_type = "functional",
    save_image = FALSE)

## End(Not run)
## Not run: 
rba_string_network_image(ids = c("TP53", "TNF", "EGFR"),
    species = 9606,
    save_image = TRUE)

## End(Not run)
## Not run: 
rba_string_network_image(ids = "9606.ENSP00000269305",
    image_format = "highres_image",
    save_image = file.path(getwd(), "TP53_network.png"))

## End(Not run)

rbioapi

User-Friendly R Interface to Biologic Web Services' API

v0.7.0

GPL-3

Authors

Moosa Rezwani [aut, cre, cph]

Initial release