I want to display an x-y scatter plot not using the ratio values derived from ion counts accumulated in ROIs but using pixel-by-pixel ratios values. I want to include only those pixels that belong to ROIs that I have drawn and classified, and I want the data-points in the scatter plot to be color-coded based on the ROI classes.
Because the number of pixels in the defined ROIs is usually large, the x-y graphs may not always be very informative (e.g. they may form several indiscernible clouds). Therefore, in addition to the x-y graph, the density of the pixels in the x-y graph is also shown as a 2D histogram (see image above). The default number of bins in this 2D histogram is 50 for both x and y dimensions.