plotEmap: Plots an EnrichmentMap in Cytoscape to visualize...

In BaderLab/POPPATHR: Population-based pathway analysis of SNP-SNP coevolution

Description

Create a network where nodes are pathway gene sets significantly enriched in two independent population-based GSEA (i.e., validated selection-enriched gene sets.) Pathways are then clustered to identify main pathways and themes of the selection-enriched gene sets.

Usage

plotEmap(
  gmt_file,
  EM_file,
  EM_group_file,
  output_folder,
  net_name = "generic",
  image_format = "png"
)

Arguments

gmt_file	(char) file path to GMT file (this needs to be absolute path name).
EM_file	(char) file path to results_EM.txt (generated by writeEmapFile.R).
EM_group_file	(char) file path to write pathway groupings as determined by EnrichmentMap.
output_folder	(char) file path to write gene set grouping file. This will be used for between-pathway SNP association analysis.
net_name	(char) name for network in Cytoscape.
image_format	(char) one of PNG, PDF, SVG, or JPEG. # Not run because requires Cytoscape to be installed and open. # plotEmap(gmt_file=gmt_file, EM_file=EM_file, output_folder=enrich_folder, net_name="generic", image_format="png").

Value

Filename of image to which EnrichmentMap is exported. Also side effect of plotting the EnrichmentMap in an open session of Cytoscape.

BaderLab/POPPATHR documentation built on Dec. 17, 2021, 9:53 a.m.