Hi All,

I am trying to make cnet plots of differentially expressed genes between 2 tissue types, looking at specific pathways identified from enrichGO analysis. When I plot this a bunch of non-significantly regulated genes are appearing as uncolored dots and I am not sure how to stop this from happening so that my plots only include significantly regulated genes within the pathway of interest. I have attached an example of one of the cnet plots generated and am hoping someone knows how to fix this problem.

Here is the code I am using for the cnet:

>selected_pathways = "response to oxidative stress"

>cnetplot(eGO2, foldChange = geneListC57mnx_chow_iWAT_vs_eWAT, showCategory = selected_pathways, circular = FALSE, colorEdge = TRUE)

And the code for generating eGO2:

>eGO2 <- enrichGO(gene          = as.character(C57mnx_chow_sorted_gene_list$ensembl_gene_id),
                 OrgDb         = org.Mm.eg.db,
                 keyType = "ENSEMBL",
                 ont           = "ALL",
                 pAdjustMethod = "BH",
                 pvalueCutoff  = 0.01,
                 qvalueCutoff  = 0.05,
                 readable      = TRUE)

The file geneListC57mnx_chow_iWAT_vs_eWAT only includes genes that have a p.adjusted > 0.05 so I am confused as to why the plot is such a mess of insignificant genes. Any help would be much appreciated!