Contrast polygenicity¶

We provide script (misc/contrast_polygenicity.py) to make the plot for contrasting degrees of polygenicity between traits. The script can be executed as follows.

Input¶

• Local SNP-heritability estimates for a number of traits.

We recommend to plot less than 10 traits at a time.

Example¶

The following is an example script to create the contrast polygenicity plot.

python $src/contrast_polygenicity.py \
    --local-hsqg-est <local SNP-heritability output trait 1>  <local SNP-heritability output trait 1> \
    --show-se --no-negative --trait-names TRAIT1 TRAIT2 \
    --out <output file name e.g. trait1_trait2_contrast.pdf>

Here --no-negative enforces any negative local estimates to 0.0 Standard error shade can be turned off by removing the --show-se flag.

The following is an example output figure.