Volcano plots with LAVAA
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A lightweight association viewer across ailments LAVAA plots are computed and available for FinnGen endpoints in PheWeb from DF10 onwards.
PheWAS associations can differ both in significance (p value) and effect size (beta or OR). We provide a viewer called a volcano plot so you can easily see the different directions of effect (doe) that certain associations may have. (Volcano plots were originally used to show expression data.)
By clicking on associations you can display the name of the phenotype and the number of cases.
The LAVAA plot also has the ability to show if the variant is in the credible set of an association by checking the PIP box.
The LAVAA plots are available for FinnGen endpoints in PheWeb from DF10 onwards.
We also provide a website where you can upload your own files as well: https://geneviz.aalto.fi/LAVAA/.
The online LAVAA tool can also enable you to edit out redundant phenotypes for publication. The download table from the PheWeb is the format of the data you need to start with.
Additionally, you can access the LAVAA code on GitHub if you wish to include it in an internal portal: https://github.com/FINNGEN/volcano_plot.
For more information visit the LAVAA tool page and the original article: LAVAA: a lightweight association viewer across ailments.
