I am using ReportingTools in conjunction with DESeq2 to create a standard HTML report of differentially expressed genes using the recommended syntax for object class DESeqDataSet. Everything works fine except the default plots use a log10 scale and autozoom. I would like to create a linear scale with a fixed origin of 0 for all counts. 

Initially I thought of passing a plotting argument directly to the publish() function. However, examining the source code, it seems this is an S4 method and the argument for scales is generated by one of the sub-functions. Therefore, is it possible to modify the vertical axis using the compiled package, or would I have to rewrite the source and compile my own version of ReportingTools?

Many thanks,

trebbiano