# 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="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-69c82476496748e5955a777715b8d577c21cfa38%2FManhattan_icon_location_in_report.png?alt=media" 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="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-2bf212ff8ac72d51b9c8ec8f5e452a6e879eeb4a%2FDSS_ManhattanPlot.png?alt=media" 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="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-305bf47418ec050cef331636a0957f3a0702dfc2%2Fdetect_diff_methylation_Manhattan.png?alt=media" 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="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-52dae6b1dcb66e262af2923444c54e075dde0c9e%2FManhattan_customize_axes.png?alt=media" alt=""><figcaption></figcaption></figure>

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-5bcb68ed056978a92a62337761550b73c4828eb1%2FManhattan_customize_statstics.png?alt=media" 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.