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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.

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