A Manhattan plot is a type of scatter plot, usually used to display data with a large number of data-points, many of non-zero amplitude, and with a distribution of higher-magnitude values. The plot is commonly used in genome-wide association studies (GWAS) to display significant SNPs.
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). The different colors of each block usually show the extent of each chromosome.
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