Manhattan Plot

The Manhattan plot is a 2D scatter plot used to visualize differentially expressed regions along genomic positions for a given comparison. The X-axis represents genomic positions across chromosomes. The Y-axis shows test statistics from the comparison.

As a prerequisite for invoking the Manhattan plot, you must run a differential test that generates regions that are differentially expressed across sample groups or a differential analysis on regions data. For examples, the Differential Methylation task using DSS caller on CpG data to generate differentially methylated regions (DMRs) or the Detect Differential Methylation task on regional data.

Once the analysis is complete, open the resulting differential task report. Click on the Manhattan plot icon, located on the left of the comparison name.

Each point on the plot represents a differentially expressed region. For Manhattan plot invoked from the Differential Methylation task using DSS caller, by default, the y-axis is abs(areaStat) test statistics.

For Manhattan plot invoked from the Detect Differential Methylation task result, by default, the y-axis is negative log10 of the p-values from the statistical test of the comparison. The black horizontal dash lines represents threshold of significant p-value, default at 0.05.

The Axes and Statistics menus within the plot allow to customize which data sources will be used for the axes as well as axis scales and significance thresholds for the plot.

Click Export button on the top of the plot, select Export image to save a PNG, SVG, or PDF image to your computer.