SkeletalVis (version 0.1.2)

view_network: 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)

Value

A visNetwork interactive network'

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.

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)