I am working on subclonal evolution of multiple myeloma. After literature survey, I found people use Fish plot to represent tumor evolution. The example of fish plot can be found here. But I am not able to interpret this plot. How this plot represent tumor evolution and subclones in tumor. Can anybody explain with example. Thanks.
Each color is a clone (set of mutations) or an individual mutation (depends on how the input data was generated). This is a cancer with the bottleneck likely being induced by a treatment (e.g. UV, chemo, drugs, etc...)
Based on the vignette this is likely an AML (leukemia).
It looks like grey are healthy cells. At day 0 a specific clone (red) existed at a low frequency (~20-40%). The patient (or cells) was then exposed to a treatment and on day 150 another measurement was taken. In this case two novel clones (subclones of red) have taken over the population. They seem to co-exist or are co-dominate clones with orange being 50-60% of the population and yellow being 30-40%.
The example says "Simple plot with multiple subclones" so: the orange and yellow populations have additional (likely mutually exclusive) mutations that were not present in the red clone - but biologically also have all the mutations in the red clone. So my first assumption was right - each color is a proxy for a set of mutations.
You could have generated the mutation data (i.e. allele frequencies) from a wide variety of sources (scRNA-Seq, exome-sequencing, PCR genotyping, etc...)