#make a gene network from enriched pathways
options(ggrepel.max.overlaps = Inf)
## convert gene ID to Symbol
edox <- setReadable(gse, 'org.Mm.eg.db', 'ENSEMBL')
p2 <- cnetplot(edox, categorySize="pvalue", showCategory=16, foldChange=gene_list, node_label="category")

I'm using the above code to try to make a gene network for some pathways enriched in my GSEA data analysis, however one of the pathways that I am interested in including is the 16th pathway in the list. Because of the number of genes involved, plotting with showCategory=16 is too cluttered. I want to write some sort of ifelse statement to plot just the 16th pathway. Or does anyone know how to specify show category as a range where the first included pathway is not the first pathway? I'm using the enrichplot library with DOSE dependencies.

Thank you for your help!

There might be a more direct method, but this works. Note that it's better to show a self-contained example that other people can run, like I do below, using the example from ?cnetplot

> library(DOSE)
> data(geneList)
> de <- names(geneList)[1:100]
> x <- enrichDO(de)
> x2 <- pairwise_termsim(x)
> as.data.frame(x2)$Description[1:16]
 [1] "urinary bladder cancer"                   
 [2] "esophageal carcinoma"                     
 [3] "stomach cancer"                           
 [4] "microcephaly"                             
 [5] "interstitial lung disease"                
 [6] "esophageal cancer"                        
 [7] "sarcoidosis"                              
 [8] "biliary tract cancer"                     
 [9] "pre-malignant neoplasm"                   
[10] "breast ductal carcinoma"                  
[11] "pulmonary sarcoidosis"                    
[12] "hypersensitivity reaction type IV disease"
[13] "endometrial carcinoma"                    
[14] "bronchiolitis obliterans"                 
[15] "in situ carcinoma"                        
[16] "thoracic aortic aneurysm"     
> cnetplot(x2, showCategory = "thoracic aortic aneurysm" )
## or let's say you want three terms, 
> cnetplot(x2, showCategory = as.data.frame(x2)$Description[c(1,5,16)])

Note that this is explained in the help page

showCategory: A number or a vector of terms. If it is a number, the
          first n terms will be displayed. If it is a vector of terms,
          the selected terms will be displayed.

The trick is figuring out how to get the terms.