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!

![enter image description here][1]


  [1]: /media/images/bebf9529-1b09-4775-98a9-fb7449f9
I think the issue is that you're creating `eGO2` with non-significant genes. Try subsetting `C57mnx_chow_sorted_gene_list` to your thresholds before sending it through `enrichGO`