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uclahs-cds / package-CancerEvolutionVisualization

Publication Quality Phylogenetic Tree Plots
https://cran.r-project.org/web/packages/CancerEvolutionVisualization/
GNU General Public License v2.0
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CP other than 1 #49

Open dan-knight opened 1 year ago

dan-knight commented 1 year ago

Discussed in https://github.com/uclahs-cds/public-R-CancerEvolutionVisualization/discussions/46

@lydiayliu Not that it really matters for the visualization, but cellular prevalence is the proportion of cells that belong to each cluster in the entire sequenced sample. The example shown (where the CP of the root node is 1) is practically impossible in real life (because there is always going to be some stromal contamination in bulk sequencing), and is more reflective of the cancer cell fraction (CCF, the proportion of cells that belong to each cluster in the tumour cells sequenced). Question is, if the root node does not have CP = 1, does the function still work?

lydiayliu commented 1 year ago

Oh I tried this, it does work (Like the x-axis is just 0-95% for example), just that the x-axis label needs to be changed if the user actually uses CCF