Visualize Interactions of Genes Involved in the Given Enriched Terms

Source: R/visualization.R

Visualize Interactions of Genes Involved in the Given Enriched Terms

visualize_term_interactions(result_df, pin_name_path, show_legend = TRUE)

Arguments

result_df

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

pin_name_path

Name of the chosen PIN or absolute/path/to/PIN.sif. If PIN name, must be one of c('Biogrid', 'STRING', 'GeneMania', 'IntAct', 'KEGG', 'mmu_STRING'). If path/to/PIN.sif, the file must comply with the PIN specifications. (Default = 'Biogrid')

show_legend

Boolean to indicate whether to display the legend (TRUE) or not (FALSE) (default: TRUE)

Value

list of ggplot objects (named by Term ID) visualizing the interactions of genes involved in the given enriched terms (annotated in the result_df) in the PIN used for enrichment analysis (specified by pin_name_path).

Details

The following steps are performed for the visualization of interactions of genes involved for each enriched term:

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

  2. the nodes of all shortest paths 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 (if provided)

See also

See visualize_terms for the wrapper function for creating enriched term diagrams. See run_pathfindR for the wrapper function of the pathfindR enrichment workflow.

Examples

if (FALSE) { # \dontrun{
result_df <- example_pathfindR_output[1:2, ]
gg_list <- visualize_term_interactions(result_df, pin_name_path = 'IntAct')
} # }