View source: R/visualization.R
visualize_terms | R Documentation |
Create Diagrams for Enriched Terms
visualize_terms(
result_df,
input_processed = NULL,
hsa_KEGG = TRUE,
pin_name_path = "Biogrid",
...
)
result_df |
Data frame of enrichment results. Must-have columns for
KEGG human pathway diagrams ( |
input_processed |
input data processed via |
hsa_KEGG |
boolean to indicate whether human KEGG gene sets were used for
enrichment analysis or not (default = |
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') |
... |
additional arguments for |
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.
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.
## Not run:
visualize_terms(result_df, input_processed)
visualize_terms(result_df, hsa_KEGG = FALSE, pin_name_path = 'IntAct')
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.