R/visualization.R
visualize_term_interactions.Rd
Visualize Interactions of Genes Involved in the Given Enriched Terms
visualize_term_interactions(result_df, pin_name_path, show_legend = TRUE)
Data frame of enrichment results. Must-have columns are: 'Term_Description', 'Up_regulated' and 'Down_regulated'
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')
Boolean to indicate whether to display the legend (TRUE
)
or not (FALSE
) (default: TRUE
)
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
).
The following steps are performed for the visualization of interactions of genes involved for each enriched term:
shortest paths between all affected genes are determined (via igraph
)
the nodes of all shortest paths are merged
the PIN is subsetted using the merged nodes (genes)
using the PIN subset, the graph showing the interactions is generated
the final graph is visualized using igraph
, colored by changed
status (if provided)
See visualize_terms
for the wrapper function
for creating enriched term diagrams. See run_pathfindR
for the
wrapper function of the pathfindR enrichment workflow.
if (FALSE) {
result_df <- example_pathfindR_output[1:2, ]
gg_list <- visualize_term_interactions(result_df, pin_name_path = 'IntAct')
}