color_kegg_pathway: Color hsa KEGG pathway

In egeulgen/pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Color hsa KEGG pathway

Description

Color hsa KEGG pathway

Usage

color_kegg_pathway(
  pw_id,
  change_vec,
  scale_vals = TRUE,
  node_cols = NULL,
  legend.position = "top"
)

Arguments

pw_id	hsa KEGG pathway id (e.g. hsa05012)
change_vec	vector of change values, names should be hsa KEGG gene ids
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

a ggplot object containing the colored KEGG pathway diagram visualization

Examples

## Not run: 
pw_id <- 'hsa00010'
change_vec <- c(-2, 4, 6)
names(change_vec) <- c('hsa:2821', 'hsa:226', 'hsa:229')
result <- pathfindR:::color_kegg_pathway(pw_id, change_vec)

## End(Not run)

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