Plot Ld In R As In Haploview

Question

[Steven]

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

Answer 1

[Khader Shameer]

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:

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:

Example figure using SNAP:

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