Create Diagrams for Enriched Terms
visualize_terms( result_df, input_processed = NULL, hsa_KEGG = TRUE, pin_name_path = "Biogrid", ... )
Data frame of enrichment results. Must-have columns for
KEGG human pathway diagrams (
input data processed via
boolean to indicate whether human KEGG gene sets were used for
enrichment analysis or not (default =
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")
additional arguments for
hsa_KEGG = TRUE, KEGG human pathway diagrams are created,
affected nodes colored by up/down regulation status.
For other gene sets, interactions of affected genes are determined (via a shortest-path
algorithm) and are visualized (colored by change status) using igraph.
Depending on the argument
hsa_KEGG, creates visualization of
interactions of genes involved in the list of enriched terms in
result_df and saves them in the folder "term_visualizations" under
the current working directory.
visualize_hsa_KEGG for the visualization function
of human KEGG diagrams. See
visualize_term_interactions for the
visualization function that generates diagrams showing the interactions of
input genes in the PIN. See
run_pathfindR for the wrapper
function of the pathfindR workflow.
## Not run: visualize_terms(result_df, input_processed) visualize_terms(result_df, hsa_KEGG = FALSE, pin_name_path = "IntAct") ## End(Not run)
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