R: How to show Correlation matrix as LD blocks similar as in haploview

Question

[Shicheng Guo]

R: How to show Correlation matrix as LD blocks similar as in haploview

Suppose we can a correlation matrix, sure, it is symmetric matrix and how can we show it as the LD block such as the output in haploview as the following:

Be careful, my input is a correlation matrix, not plink or any other snp dataset.

Still not good.

Answer 1

[AndreiR]

Maybe:

Plot Ld In R As In Haploview

would help.

In this vignette there is an alternative not so like haploview but maybe help:

http://www.bioconductor.org/packages/release/bioc/vignettes/trio/inst/doc/trio.pdf