I am trying to plot the co-linearity of marker locations on multiple physical and genetic maps.

I am not trying to improve the physical maps via the genetic maps, I just want to plot the co-linearity to see the discordance and the few discordances.

I have a reference genome based on short reads, a reference genome (of the same biomaterial) based on long reads, and multiple genetic maps.

In excel I can plot in a XY plot if the markers are all on the same chromosome and the same linkage group. If markers however go to multiple linkage groups (or multiple chromosomes), then the XY plot does not make sense anymore.

So I was hoping to make the kind if plot as shown here in the example. Is there an easy tool to make these kind of plots, without running scaffolding ? (i.e. consider the maps to be final)