Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.
This was already a problem in PhyloWGS, but there was only a single tree and 2-3 tables. in the pairtree, after running the example
I am swamped by different tables and different colours without explanation.
For example tables A_B, B_A, diff_branches, clusterstats, cocluster, ML relations. What is the diversity index? What is the difference between Tree-implied, data-implied and interleaved subclonal frequencies? Why some corrected VAFs show NAN when I hover over them?
Please, document the output.
Also, if pairtree can export this output as a (vectorized) PDF/SVG or export individual images, that would be best. Methods to export HTML to SVG/PDF do not always work well. For example, I spend quite a lot of time trying various libraries to export the PhyloWGS output and had to resort to manually deleting a particular interactive elements and re-saving the HTML.
This was already a problem in PhyloWGS, but there was only a single tree and 2-3 tables. in the pairtree, after running the example I am swamped by different tables and different colours without explanation.
For example tables A_B, B_A, diff_branches, clusterstats, cocluster, ML relations. What is the diversity index? What is the difference between Tree-implied, data-implied and interleaved subclonal frequencies? Why some corrected VAFs show NAN when I hover over them?
Please, document the output.
Also, if pairtree can export this output as a (vectorized) PDF/SVG or export individual images, that would be best. Methods to export HTML to SVG/PDF do not always work well. For example, I spend quite a lot of time trying various libraries to export the PhyloWGS output and had to resort to manually deleting a particular interactive elements and re-saving the HTML.