Dear RNA-Seq community!
I am currently plotting the results of a CuffDiff run with cummeRbund. I have been able to produce some nice scatterplots on all genes of a particular gene ontology we are interested in. What i was wondering was whether or not it is possible to take a subset of these genes and highlight these points in the scatterplot with a different colour. I understand this is relatively easy to do if you would like highlight statistically significant genes on volcano plots but i wanted to specify the genes which are highlighted rather than just highlighting on the basis of statistical significance (which i don't really trust anyway as i am working with non-replicated data).
I am currently plotting the results of a CuffDiff run with cummeRbund. I have been able to produce some nice scatterplots on all genes of a particular gene ontology we are interested in. What i was wondering was whether or not it is possible to take a subset of these genes and highlight these points in the scatterplot with a different colour. I understand this is relatively easy to do if you would like highlight statistically significant genes on volcano plots but i wanted to specify the genes which are highlighted rather than just highlighting on the basis of statistical significance (which i don't really trust anyway as i am working with non-replicated data).