An IGV scatter plot displays the relationship between two sets of sample tracks of continuous-value data in a genomic region. Supported data types include gene expression, copy number data, and methylation data. Use the region of Interest tool to identify the region boundaries, and then click on the red bar at the top of the region to bring up the menu. If you have loaded data of any of the supported data types, you will see a "Scatter Plot..." option in the menu. Click on this option to bring up a separate scatter plot window. The example shown below uses data loaded from the IGV server by selecting The Cancer Genome Atlas>GBM Subtypes (Verhaak et. al.) from the datasets available with the hg18 reference genome.