# Manhattan Plot

The Manhattan plot is a common way to visualize p-values or log-odds ratios for GWAS studies across genomic coordinates.

The starting point for a Manhattan plot is a spreadsheet with SNPs on rows and p-values or log-odds ratios in a column. If beginning with p-values, you will need to convert the p-values to -log10(p-value).

* Select the column with p-values
* Select **Transform** form the main toolbar
* Select **Normalization & Scaling**
* Select **On Columns...**
* In the *Normalization* tab, set *Base* of the *Log(x + offset)* to **10**
* Select **OK**
* Go to **Transform > Normalization & Scaling > On Columns...** again
* Select the **Add/Mul/Sub/Div** tab
* Set *Multiply by Constant* to **-1**
* Select **OK**

The column now contains -log10(p-value).

We can now invoke the initial plot.

* Select **View** from the main toolbar
* Select **Genome View**

The *Genome View* tab will open. This plot will need to be configured.

* Select (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8686f111655525c6027f24eb07460a3a65b27fe2%2Fimage2017-8-29%2013_10_8.png?alt=media)) from the plot command bar
* Select the **Profiles** tab
* Remove any unwanted profiles
* Select **Add profile**
* Select **Column**
* Select the column with the -log10(p-value) or logs-odds ratio values from the drop-down menu
* Select **Value** for *Color by*
* Select **point** from the *Style* drop-down menu
* Select **OK** to add the profile
* Select **OK** to close the *Configure Plot Properties* dialog

The plot will now show a Manhattan plot (Figure 1).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-54bfee0481745c737ea534ee2c522360d916fe8a%2FManhatten_plot.png?alt=media)

Figure 1. Customized Genome View showing genomic locations on the x-axis and -log10(P-values) of SNPs on the y-axis (Manhattten plot). Each dot represents a single SNP. The Cytoband is shown along the bottom of the plot

It is also possible to display multiple chromosomes at the same time.

* Select **Show All** in the upper-right hand corner of the plot

This displays all chromosomes vertically. We can display them horizontally for a better view.

* Select ![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-3248fddaa31c564ec1c6bad46f6a2f6e705da5a5%2Fimage2017-10-27%2016_58_52.png?alt=media) to open the *Configure Plot* dialog
* Select **Genome in line** for *Layout*
* Select **OK**

To further improve the genome-wide view, we can remove the cytoband, remove the genomic position label, color points by chromosome, and increase point size.

* Select **Cytoband** in the upper right-hand corner
* Select ![alt text](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8686f111655525c6027f24eb07460a3a65b27fe2%2Fimage2017-8-29%2013_10_8.png?alt=media)
* Select the **Axes** tab
* Deselect **Show Base Pair Labels**
* Select **Profiles**
* Select **Configure**
* Set *Color By* to a column with chromosome for each SNP/loci as a category
* Set *Shape Size* to **5.0**
* Select **OK** to close the *Configure Profile* dialog
* Select **OK** to apply changes

The plot will appear as shown (Figure 2).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-1e6232cada1c5db57e2be908fe716953dca62dc8%2Fimage2017-10-27%2017_9_30.png?alt=media)

Figure 2. Full genome Manhattan plot

For details on *Genome View* see **Chapter 6: The Pattern Visualization System** in the Partek User's Manual.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.