https://rdrr.io/bioc/maftools/man/plotClusters.html
I am trying to better understand how to interpret the graph output from plotClusters in maftools.
I can't find too many resources explaining this in the docs. If anyone has a resource or paper I can refer to, I would appreciate it.
For now, from what I understand each bar at the top is supposed to represent a different clone in a tumor based on the VAF clusters at the bottom. The clusters at the bottom represent specific mutations in certain genes and the VAF at which they occur. So the bars with lower VAF represent subclones that arose later on in the tumor b/c that VAF is lower? And the bars with gene mutations that have higher VAF represent older clones that originated earlier in the tumorigenesis process. The line on the graph is supposed to be the density (?) of the cluster, as in, how many mutations it was able to find in a cluster of genes? I am really not sure about the line...
And the MATH score is a loose interpretation of how "bad" the prognosis of a tumor is, with a higher MATH score meaning worse outcome.
