Visualize Human KEGG Pathways

Visualize Human KEGG Pathways

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

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