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.
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
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"))
}