> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.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="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.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://help.bioinsight.illumina.com/icm/analyses/analysis-functionality/data-viewer/manhattan-plot.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.