readcluster

The readcluster() function performs a gene set enrichment analyses with the help of clusterProfiler. Also it generates a new file for each new cluster which contains all modalities and all edges which can be found in the matrix before the reduction.

readcluster(clustermember = block_member.csv, matrix = matrix, minclustersize = 9, minp.adjust = 0.01)

argument	function	default
clustermember	blockmember.csv file from Graph.py
matrix	matrix from calcscorematrix()
minclustersize	minimum size of the cluster to be given to the enrichment analyses	9
minp.adjust	minimum p.adjust for the enrichment analyses	0.01

The request against the KEGG database generates a PDF file for all genes of the graph and for every found clusters. It contains a dotplot, goplot, barplot and a cnetplot (shown below).