SNP visualization

If at any point you need help, you can watch the movie to see these instructions being carried out.

1. Open the snp_analysis.txt file. One way to do this is to drag and drop the file onto the DecisionSite window.

1. DecisionSite automatically displays a scatter plot. Each row in the data set is one marker on the plot.

2. Create a table visualization by selecting New Table from the Visualization menu. The Pvalue column contains the significance value for the various SNPs. The Pvalues were calculated prior to loading the data into DecisionSite and are based on the density of certain genotypes in nearby chromosome regions.

3. Create a chromosome view visualization. The following steps will walk you through creating a visualization that shows chromosomes 1 through 22 and the SNPs on each chromosome.

1. Choose Visualization->New Scatter Plot. The X axis already has the value we want, Physical Position.
2. Change the Y axis of the scatter plot to Chromosome.
3. Right-click on the Y axis labels and choose More Labels (do this step twice in order to place labels on each chromosome).
4. If the Legend is not visible, choose View->Legend from the DecisionSite View menu.
5. Right-click on the visualization and choose "Properties"
6. Select the "Markers" tab in the Properties window
   
7. In the "Shape" section, click the Customize button and change the marker shapes from squares to vertical bars.
8. In the "Color" section, set the coloring to the Pvalue column.
9. In the "Size" section, set the sizing to the Pvalue column.
10. Close the "Properties" window.

The scatter plot now shows you where the SNPs are on each chromosome. The large blue markers indicate statistically significant SNPs. You can mouse over or click on bars to get information about SNPs of interest.

You can see that there is an interesting/significant region near the middle of chromosome 3 as indicated by the larger blue markers that are clustered together there.