visualize_hsa_KEGG: Visualize Human KEGG Pathways

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Visualize Human KEGG Pathways

Description

Visualize Human KEGG Pathways

Usage

visualize_hsa_KEGG(
  hsa_kegg_ids,
  input_processed,
  scale_vals = TRUE,
  node_cols = NULL,
  quiet = TRUE,
  key_gravity = "northeast",
  logo_gravity = "southeast"
)

Arguments

hsa_kegg_ids	hsa 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.
quiet	If TRUE, suppress status messages (if any), and the progress bar while downloading file(s)
key_gravity	gravity value (character) for the color key legend placement (see gravity_types)
logo_gravity	gravity value (character) for the logo placement (see gravity_types)

Value

Creates colored visualizations of the enriched human KEGG pathways and saves them in the folder 'term_visualizations' under the current working directory.

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: 
visualize_hsa_KEGG(hsa_kegg_ids, input_processed)

## End(Not run)

pathfindR documentation built on Oct. 9, 2023, 1:07 a.m.