Combined Results Graph
combined_results_graph(
combined_df,
selected_terms = "common",
use_description = FALSE,
layout = "stress",
node_size = "num_genes"
)| combined_df | Data frame of combined pathfindR enrichment results |
|---|---|
| selected_terms | the vector of selected terms for creating the graph
(either IDs or term descriptions). If set to |
| use_description | Boolean argument to indicate whether term descriptions
(in the "Term_Description" column) should be used. (default = |
| layout | The type of layout to create (see |
| node_size | Argument to indicate whether to use number of significant genes ("num_genes") or the -log10(lowest p value) ("p_val") for adjusting the node sizes (default = "num_genes") |
a ggraph object containing the combined term-gene graph.
Each node corresponds to an enriched term (orange if common, different shades of blue otherwise),
an up-regulated gene (green), a down-regulated gene (red) or
a conflicting (i.e. up in one analysis, down in the other or vice versa) gene
(gray). An edge between a term and a gene indicates
that the given term involves the gene. Size of a term node is proportional
to either the number of genes (if node_size = "num_genes") or
the -log10(lowest p value) (if node_size = "p_val").
combined_results <- combine_pathfindR_results(RA_output,
RA_comparison_output,
plot_common = FALSE)
#> You may run `combined_results_graph()` to create visualizations of combined term-gene graphs of selected terms
g <- combined_results_graph(combined_results, selected_terms = sample(combined_results$ID, 3))