Question: Plotting marker location co-linearity between multiple physical and genetic maps
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gravatar for William
5 months ago by
William4.7k
Europe
William4.7k wrote:

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)

41438-2017-11-Fig3-HTML

ideogram plotting • 151 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by William4.7k
2
gravatar for William
5 months ago by
William4.7k
Europe
William4.7k wrote:

RIdeogram seems to be able to do what I am looking for:

https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html

2way

3way

ADD COMMENTlink written 5 months ago by William4.7k
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