gravatar for Ali May

2 hours ago by

The Netherlands

Hi,

I'm using the groupGO command in clusterProfiler to group a subset of (e.g. significantly DE) genes under GO terms. I would like to visualise the results where the relationship between the GO terms, the genes, and their fold changes are shown. To this end, I'm trying to use the cnetplot function, but the plot I get is incorrect (contains nonsensical terms/nodes). I believe this is because the input to cnetplot is supposed to be an enrichment result object, not a groupGO object.

Is there a way to achieve this, i.e. visualising results from groupGO where individual genes and their fold changes etc. are displayed with their ontology terms? The appoach I'm taking which gives non-sensical cnetplots plots is the following:

        ggo <- groupGO(gene     = filt_gene_fc_entrezid,
                       OrgDb    = org.EcK12.eg.db,
                       ont="BP",
                       level    = 3,
                       readable = TRUE)

        cnetplot(ggo, showCategory=5,
                      categorySize="pvalue",
                      foldChange=geneList,
                      order=TRUE)

where geneList is an object that has the fold change information for genes in filt_gene_fc_entrezid.

Thanks in advance,
Ali

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Ali May0



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