> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/icm/analyses/analysis-functionality/data-viewer/manhattan-plot.md).

# 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](https://help.multiomics.illumina.com/icm/analyses/analysis-functionality/task-menu/statistics/correlation-analysis-2) task using DSS caller on CpG data to generate differentially methylated regions (DMRs) or the [Detect Differential Methylation](https://help.multiomics.illumina.com/icm/analyses/analysis-functionality/task-menu/methylation-analysis/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.

<figure><img src="/files/I6xKecToIxMH9WWuGuO9" alt=""><figcaption></figcaption></figure>

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.

<figure><img src="/files/KX3jPSuVyagK5V899AwU" alt=""><figcaption></figcaption></figure>

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.

<figure><img src="/files/TbolKk7VLosC0zT34R4z" alt=""><figcaption></figcaption></figure>

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.

<figure><img src="/files/WiN1u4sfroWnJ4reihpK" alt=""><figcaption></figcaption></figure>

<figure><img src="/files/bkdxVR4JDiCbynwubakG" alt=""><figcaption></figcaption></figure>

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


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