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)Arguments of the readcluster() function.
| 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 the genes of every found cluster. It contains a dotplot, goplot, barplot and a cnetplot (shown below).
The generated files with all modalities and edges can be analyzed with the help of Graph_subcluster.py