Visualize Human KEGG Pathways
visualize_KEGG_diagram(
kegg_pw_ids,
input_processed,
scale_vals = TRUE,
node_cols = NULL,
legend.position = "top"
)
KEGG ids of pathways to be colored and visualized
input data processed via input_processing
should change values be scaled? (default = TRUE
)
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.
the default position of legends ("none", "left", "right", "bottom", "top", "inside")
Creates colored visualizations of the enriched human KEGG pathways and returns them as a list of ggplot objects, named by Term ID.
See visualize_terms
for the wrapper function for
creating enriched term diagrams. See run_pathfindR
for the
wrapper function of the pathfindR enrichment workflow.
if (FALSE) {
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)
}