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Visualizing tumor evolution with the fishplot package for R

By Christopher Miller, Joshua McMichael, Ha X Dang, Christopher A Maher, Li Ding, Timothy J Ley, Elaine R. Mardis, Richard K Wilson

Posted 15 Jun 2016
bioRxiv DOI: 10.1101/059055 (published DOI: 10.1186/s12864-016-3195-z)

Background: Massively-parallel sequencing at depth has enabled tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture can inform therapeutic response and resistance. Robust and intuitive data visualizations can greatly aid these interpretations, especially in cases with multiple timepoints . Current data visualization methods are typically manual and laborious, and often only approximate subclonal fractions. Results: We have developed an R package that accurately and intuitively displays changes in clonal structure over time. It requires simple input data and produces illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication. Conclusions: The simplicity, power, and flexibility of this tool make it valuable for visualizing tumor evolution, and it has potential utility in both research and clinical settings. Fishplot is available at https://github.com/chrisamiller/fishplot

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