mRNA expression (RNAseq) scatter plot issues

The y-axis of the plot is just the different categories (non-conserving, other, etc)

However, are you asking what does the y-axis represent within a category (that is to say, within a violin plot)?

If so, the answer is: the y value within a violin plot is randomly assigned. The points are “jittered” on the y-axis to avoid overplotting and allow you to see individual points. There is no meaning to the y-value within each violin.

Thanks,
Phil