Visualizing local estimates¶

This page describes script to visualize local SNP-heritability estimates and local genetic covariance estimates.

Local SNP-heritability estimates¶

We provide script (misc/local_hsqg_manhattan.py) that makes Manhattan-style plot for visualizing local SNP-heritability estimates. The script can be executed as follows.

python misc/local_hsqg_manhattan.py \
    --local-hsqg-est <local SNP-heritability output> \
    --out <output file name e.g. trait1_local_hsqg.pdf> \
    --trait-name TRAIT1

There following is an example figure generated by the visualization tool. Here, colored bars represent loci that have significant local SNP-heritability.

local SNP-heritability Manhattan plot

Local genetic covariance estimates¶

We provide script (misc/local_rhog_manhattan.py) that makes Manhattan-style plot for visualizing local genetic covariance estimates. The script can be executed as follows.

python misc/local_rhog_manhattan.py \
    --local-rhog-est <local genetic covariance estimates output> \
    --local-hsqg-est <local SNP-heritability output trait 1>  <local SNP-heritability output trait 2> \
    --out <output file name e.g. trait1_trait2_local_rhog.pdf> \
    --trait-names TRAIT1 TRAIT2

Similarly, colored bars represent loci that have significant local genetic covariance.

local genetic covariance Manhattan plot