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Genomics Suite Documentation

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Numbered figure captions
SubtitleTextCustomized 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
AnchorNameManhatten 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 Image Added 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 Image Added 
  • 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).

 

Numbered figure captions
SubtitleTextFull genome Manhattan plot
AnchorNameManhattan Plot

Image Added

 

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

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