view_network {SkeletalVis} | R Documentation |
View the OATarget gene network
Description
This function visualises the protein-protein interaction network surrounding a specified gene, highlighting those genes that have been experimentally pertubated and the resulting effect of OA.
Usage
view_network(skeletalvis, query, hide_unannotated = TRUE, physics = TRUE)
Arguments
skeletalvis |
A string specifying the path to the directory containing the "network.RDS" file. |
query |
The name of the gene to visualise within the network. |
hide_unannotated |
A logical value indicating whether to hide nodes with no measured effect (default: TRUE). |
physics |
A logical value indicating whether to enable physics for the network (default: TRUE). |
Details
The function extracts the subnetwork surrounding the specified gene. Nodes are coloured based on their effect ("Protective", "Detrimental", "Ambiguous", "No effect", or "Not measured"). If 'hide_unannotated = TRUE', nodes not yet studied are removed unless they are the target gene.
Value
A visNetwork interactive network'
Examples
# Specify the path to the skeletalvis directory
skeletalvis <- load_skeletalvis(demo=TRUE)
# Visualize the network for a specific gene
vis <- view_network(skeletalvis, "COL2A1")
# Show unannotated nodes
vis_filtered <- view_network(skeletalvis, "COL2A1", hide_unannotated = FALSE)