Excel: How to plot a stacked scatter set

Excel can do this pretty easily.

1. Create a standard Column Chart (not stacked). It can also be done with an area chart.
2. Add your two data series (assuming a chart similar to the sample you shared).
3. In your Select Data Source > Legend Entries (Series) make sure the series you want shown "on top" is at the bottom of the list (the series are drawn in order top to bottom, so the first series will be at the "back" when drawn in the chart).
4. Format your data series to Series Overlap = 100% and Gap Width = 0%.
5. Format your "front or top" series to be transparent. You'll then see the "back or bottom" series through the transparency.

For best effect, I adjust the transparency of both series. For multiple series, I'd start with a transparency setting that adds to 100% when all the series are overlapped (e.g. two series, each at 50%, or three series, each at 33%). Then adjust to taste.

Alternatively, if you want to emphasize the intersection, you could create a third data series and plot that as an overlay, with a stronger color to highlight it, like this:

Another possibility, using your sample data:

Here's a small multiples sample of the individual components from the sample above:

And with a third phase added

From my understanding of your question, you want to draw a line chart with two lines (sense and antisense) separated by the 0 axis and each line contains data points for each Chromosome. Just like the chart shows below?

Please comment me if this chart is right. I made this chart using an Excel add-in called Funfun, it allows me to use JavaScript directly in Excel so I could use Chart.js library to plot this chart from the data in the spreadsheet. You could check the code on the link below.

https://www.funfun.io/1/edit/5a2d3865cdeaed4cdfca615f

You could also connect the link above to your excel so all the codes and chart will be directly loaded into your Excel. Here are some screenshots of what it looks like.

Disclosure: I'm a developer of Funfun