Create Diagrams for Enriched Terms
visualize_terms(
result_df,
input_processed = NULL,
is_KEGG_result = TRUE,
pin_name_path = "Biogrid",
...
)Data frame of enrichment results. Must-have columns for
KEGG human pathway diagrams (is_KEGG_result = 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 is_KEGG_result = FALSE
boolean to indicate whether 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_KEGG_diagram (used
when is_KEGG_result = TRUE) or visualize_term_interactions
(used when is_KEGG_result = FALSE)
Depending on the argument is_KEGG_result, creates visualization of
interactions of genes involved in the list of enriched terms in
result_df. Returns a list of ggplot objects named by Term ID.
For is_KEGG_result = TRUE, KEGG 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_KEGG_diagram for the visualization function
of 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) { # \dontrun{
input_processed <- data.frame(
GENE = c("PARP1", "NDUFA1", "STX6", "SNAP23"),
CHANGE = c(1.5, -2, 3, 5)
)
result_df <- example_pathfindR_output[1:2, ]
gg_list <- visualize_terms(result_df, input_processed)
gg_list2 <- visualize_terms(result_df, is_KEGG_result = FALSE, pin_name_path = 'IntAct')
} # }