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Plot Ld In R As In Haploview

Dear all,

I am trying to find a R package to plot LD blocks.

I found LDheatmap package but I would prefer a graphical representation as in haploview with LD blocks, and options to add lines or select markers on the graph.

Thank you for your help.

Steven

r visualization linkage haploview
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updated by Biostar Biostar • written by Steven • Steven

1 answer

If you are particular about an R package, I would like to suggest snp.plotter package. See snp.plotter reference manual here.

Example plot from snp.plotter:

alt text

In addition, I would like to suggest LocusZoom or SNAP for visualization of LD blocks.

There is a web-interface and standalone package available for LocusZoom.

Example figure using LocusZoom:

alt text

Example figure using SNAP:

alt text

Manuscript describing snp.plotter here, LocusZoom here and SNAP here.

• 117 views • link
written by Khader Shameer Khader Shameer

Thank you! I've shared this tip with my colleagues.

• 0 views • link
written by Larry_Parnell Larry_Parnell

Thanks, both tools look amazing! Going to play around with them!

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written by Sander Timmer Sander Timmer

This is really cool, kudos to the authors.

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written by 2184687-1231-83- 2184687-1231-83-

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