We have developed a set of visualization tools. The currently available tools are PheWAS-View, Synthesis-View, and PhenoGram. They can be used through the web interface on this site or downloaded as standalone scripts.
The exploration of data in a PheWAS effort presents several challenges, including the need for data visualization to assist with interpretation of the data. GWA studies of a single or limited number of traits lend themselves to Manhattan plots where p-values for every test of association are plotted by chromosomal location (x-axis) and the level of significance is visualized easily (y-axis). Such a plot does not present the complex relationships that exist between both genotypes and phenotypes in PheWAS. Therefore, to visualize the complex results of PheWAS, we have developed PheWAS-View, software that can be used to create visual summaries of the SNP, gene, phenotype, and association information resulting from these studies. Using specialized tools such as PheWAS-View to investigate results on a larger summary level as well as the individual result level is key for interpretation, analysis, and sharing of PheWAS results. While this tool was developed specifically for PheWAS, it could be used in other high throughput bioinformatics data where thousands of association results are being explored.
Synthesis-View was extended from the previous software "LD-Plus" which also uses a flexible data display format of multiple data "tracks" that can be viewed. Within Synthesis-View, through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related information such as genetic effect size and summary phenotype information, is plotted according to user preference. Through these data visualizations, rapid comparisons of multiple forms of information are possible, not easily achievable through reviewing results in tabular form alone.