Look, all these plotting packages are essentially just wrappers around ggplot, meaning they accept whatever you give them given it's in the expected format. If you want to only plot genes above a certain baseMean then filter your DESeq2 results table for that baseMean and then pass the output to the plotter. By the way, the baseMean is not necessarily a filter for expression level as it is the average for a gene across all samples. A baseMean can be low because 3 groups do not express a gene but one group expresses or moderately. DESeq2 is aware of that while calculating stats so best would be to either use all genes or exclude genes with low power as e.g. identified by running edgeR::filterByExpr() before the DE analysis. It is not standard to filter for baseMean for what's worth.