Though originally applied in the context of two channel DNA microarray gene expression data, MA plots are also used to visualise high-throughput sequencing analysis.
An improved method, which is basically a scaled, 45 degree rotation of the R vs. G plot is an MA-plot.
MA plots are then used to visualize intensity-dependent ratio of raw microarray data (microarrays typically show a bias here, with higher A resulting in higher |M|, i.e. the brighter the spot the more likely an observed difference between sample and control).
The MA plot puts the variable M on the y-axis and A on the x-axis and gives a quick overview of the distribution of the data.
Several Bioconductor packages, for the R software, provide the facility for creating MA plots.