visualize_KEGG_diagram: Visualize Human KEGG Pathways

In egeulgen/pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Visualize Human KEGG Pathways

Description

Visualize Human KEGG Pathways

Usage

visualize_KEGG_diagram(
  kegg_pw_ids,
  input_processed,
  scale_vals = TRUE,
  node_cols = NULL,
  legend.position = "top"
)

Arguments

kegg_pw_ids	KEGG ids of pathways to be colored and visualized
input_processed	input data processed via input_processing
scale_vals	should change values be scaled? (default = TRUE)
node_cols	low, middle and high color values for coloring the pathway nodes (default = NULL). If node_cols=NULL, the low, middle and high color are set as 'green', 'gray' and 'red'. If all change values are 1e6 (in case no changes are supplied, this dummy value is assigned by input_processing), only one color ('#F38F18' if NULL) is used.
legend.position	the default position of legends ("none", "left", "right", "bottom", "top", "inside")

Value

Creates colored visualizations of the enriched human KEGG pathways and returns them as a list of ggplot objects, named by Term ID.

See Also

See visualize_terms for the wrapper function for creating enriched term diagrams. See run_pathfindR for the wrapper function of the pathfindR enrichment workflow.

Examples

## Not run: 
input_processed <- data.frame(
  GENE = c("PKLR", "GPI", "CREB1", "INS"),
  CHANGE = c(1.5, -2, 3, 5)
)
gg_list <- visualize_KEGG_diagram(c("hsa00010", "hsa04911"), input_processed)

## End(Not run)

egeulgen/pathfindR documentation built on May 8, 2024, 8:40 a.m.