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 () 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).

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 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
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).

Figure 2. Full genome Manhattan plot

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

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