For GSEA analysis, we are familar with the above figure which shows the running enrichment score. But for most of the software, it lack of visualization method to summarize the whole enrichment result.
Here is an example of using
enrichMap which is good to visualize relationship among enriched gene sets.
cnetplot excel on visualizing relationship among gene sets and corresponding core genes.
dotplot was previously implemented in
DOSE to visualize hypergeometric test result. I modified it to support GSEA result.
.sign was reserved for the sign of
NES (activated for NES > 0 and suppressed for NES < 0). We can pass
split parameter and then it will apply
showCategory by splitting the results. The following example plot 30 activated and 30 suppressed enriched disease sets.
Count is the number of core genes and
G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609.