Map differential expression results to nodes

Usage

map_results_to_graph(
  g,
  de_results,
  feature_column = NULL,
  value_column = NULL,
  palette = "RdBu",
  verbose = FALSE
)

Arguments

g: An igraph object representing the pathway.
de_results: Named list of differential expression results.
feature_column: Column name in de_table containing KEGG IDs (if de_results is a single data.frame).
value_column: Column name in de_table containing values to map (if de_results is a single data.frame).
palette: Color palette for node coloring (default: "RdBu").
verbose: Whether to print progress messages (default: TRUE).

Value

An igraph or visNetwork object with mapped results.

Details

This function can be used to map the differential expression results to the graph, the input of the graph must be the output of the function kegg_to_graph in the igraph format. The results to be mapped can be provided either as a list or as a single data.frame. If a single data.frame is provided, the default column names for KEGG IDs and values are 'KEGG_ids' and 'log2FoldChange', respectively, but these can be changed using the feature_column and value_column parameters.

Examples

pathway <- "hsa04110" # Example pathway ID
graph <- kegg_to_graph(pathway_id = pathway)
# Example differential expression results
de_results <- data.frame(
  KEGG_ids = c("hsa:1234", "hsa:5678", "cpd:C00022"),
  log2FoldChange = c(1.5, -2.0, 0.5)
)
vis_graph <- map_results_to_graph(graph,
  de_results,
  feature_column = "KEGG_ids",
  value_column = "log2FoldChange"
)
#> Using provided value_column: 'log2FoldChange'
#>  and provided feature_column: 'KEGG_ids'.
#> de_results provided as a single data.frame.