Color hsa KEGG pathway

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

if (FALSE) { # \dontrun{
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)
} # }