pathfindR (version 1.3.0)

visualize_pw_interactions: Visualize Interactions of Genes Involved in the Given Pathways

Description

Visualize Interactions of Genes Involved in the Given Pathways

Usage

visualize_pw_interactions(result_df, pin_name_path)

Arguments

result_df

Data frame of enrichment results. Must-have columns are: "Pathway", "Up_regulated" and "Down_regulated"

pin_name_path

Name of the chosen PIN or path/to/PIN.sif. If PIN name, must be one of c("Biogrid", "GeneMania", "IntAct", "KEGG"). If path/to/PIN.sif, the file must comply with the PIN specifications. Defaults to Biogrid.

Value

Creates PNG files visualizing the interactions of genes involved in the given pathways (annotated in the `result_df`) in the PIN used for enrichment analysis (specified by `pin_name_path`). The PNG files are saved in the folder "pathway_visualizations" under the current working directory.

Details

The following steps are performed for the visualization of interactions of genes involved in the given pathways:

1. shortest paths between all affected genes are determined (via `igraph`)

2. the nodes of all shortest pathways are merged

3. the PIN is subsetted using the merged nodes (genes)

4. using the PIN subset, the graph showing the interactions is generated

5. the final graph is visualized using `igraph`, colored by changed status and saved as a PNG file.

See Also

See visualize_pws for the wrapper function for creating pathway diagrams. See run_pathfindR for the wrapper function of the pathfindR workflow.

Examples

# NOT RUN {
visualize_pw_interactions(result_df, pin_name_path = "IntAct")
# }