Here's the documentation page for the scatter command: https://cnvkit.readthedocs.io/en/stable/plots.html

The segment lines are now orange instead of red (for colorblind accessibility), but the interpretation is the same.

• Gray dots are the individual data points in the .cnr file
• Orange lines are the segments in the .cns file.

In the .call.cns file that is also produced by the batch command, the segments with neutral copy number are flagged and will be plotted as gray lines instead of orange, so that you can focus on the orange lines when interpreting genomic alterations.

If the sample is very noisy, or there is severe genome instability, the segmentation results (.cns) may include many short segments, and these can look like dots in the scatter plot.