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 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 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 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.

Additional Assistance

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