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 (hsa_kegg = TRUE) are: 'ID' and 'Term_Description'.
Must-have columns for the rest are: 'Term_Description', 'Up_regulated' and
'Down_regulated'
input data processed via input_processing,
not necessary when hsa_KEGG = FALSE
boolean to indicate whether human KEGG gene sets were used for
enrichment analysis or not (default = TRUE)
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 visualize_hsa_KEGG (used
when hsa_kegg = TRUE) or visualize_term_interactions
(used when hsa_kegg = FALSE)
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.
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.
See 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.
if (FALSE) {
visualize_terms(result_df, input_processed)
visualize_terms(result_df, hsa_KEGG = FALSE, pin_name_path = 'IntAct')
}