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Map continuous values to graph nodes

Source: R/network_operations.R
map_results_to_graph.Rd

Map differential expression results to nodes

Usage

map_results_to_graph(
  g,
  de_results,
  feature_column = NULL,
  value_column = NULL,
  verbose = FALSE,
  palette = NULL,
  palette_limit = NULL,
  palettes_list = list(NA_character_),
  palettes_limits_list = c(NA_real_)
)

Arguments

g

An igraph object representing the KEGG pathway graph.

de_results

A data frame or a list of data frames containing differential expression results

feature_column

Name of the column in de_results that contains KEGG IDs

value_column

Name of the column in de_results that contains values to map

verbose

Logical indicating whether to print verbose messages (default: FALSE)

palette

Optional color palette for mapping values (default: NULL, will use a default palette)

palette_limit

Optional numeric limit for the color palette (default: NULL, will be determined from data)

palettes_list

Optional list of color palettes if de_results is a list (default: NULL)

palettes_limits_list

Optional list of numeric limits for multiple palettes if de_results is a list (default: NULL)

Value

An igraph object with differential expression results mapped to node attributes

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 create_kegg_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 that it will look for are 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 <- create_kegg_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"
)
#> de_results provided as a single data.frame. Using provided value_column: 'log2FoldChange' and feature_column: 'KEGG_ids'.