Plotting 2D point density in kpPoints

[MikeEHMatson]

Hello, I was wondering if you had any suggestions as to how kpPoints might plot point density in a similar way to ggplot2? We have points of estimated copy number in 100kb bins across chromosomes, and it's difficult to determine whether or not outliers (CN > 4, 5, 6, etc...) are a minority of points.

Thanks, Mike

[bernatgel]

Hi Mike,

We do not have the option of reprensenting the point density in a similar way ggplot2 have. I can see your use case and it might make sense to add it in the future, but at the moment there's no way of doing it. As an aproximation you could use kpPoints with a semi-transparent color (e.g. "#FFAAAA44" for a semitransparent red) so the color would be more saturated where points overlap and outliers would almost disappear visually.

Would it work for you?

I'll add the density plot to our TODO list, but I cannot give you any estimated time frame.