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oncogenetics / LocusExplorer

An interactive graphical illustration of genetic associations and their biological context
MIT License
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R3.m1 Plot settings, SNP filter, -log10 p-value #58

Closed zx8754 closed 9 years ago

zx8754 commented 9 years ago

Plot settings, SNP filter, -log10 p-value

For the -log10 p value scale, it might make sense to display which p-value the transformed values correspond to.

zx8754 commented 9 years ago

For Manhattan plots it is a common practice to show p-values on Y axis as -log10() scale.

Manhattan plots (wikipedia)

In GWAS Manhattan plots, genomic coordinates are displayed along the X-axis, with the negative logarithm of the association P-value for each single nucleotide polymorphism (SNP) displayed on the Y-axis, meaning that each dot on the Manhattan plot signifies a SNP. Because the strongest associations have the smallest P-values (e.g., 10−15), their negative logarithms will be the greatest (e.g., 15).