Combined Results Graph
combined_results_graph(
combined_df,
selected_terms = "common",
use_description = FALSE,
layout = "stress",
node_size = "num_genes"
)Data frame of combined pathfindR enrichment results
the vector of selected terms for creating the graph
(either IDs or term descriptions). If set to "common", all of the
common terms are used. (default = "common")
Boolean argument to indicate whether term descriptions
(in the "Term_Description" column) should be used. (default = FALSE)
The type of layout to create (see ggraph for details. Default = "stress")
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))