Comments (1)
saikatds-bd
commented on August 25, 2024
Hi! I know it is too late and probably you have already sorted it out, but writing it for others from my experience (and also to know if I misunderstood anything). I think the missing subclones are due to the threshold set in the uphyloplot2 python script. For example, I got less subclones in the uphyloplot2 output when I used "python uphyloplot2.py -c 10", even less by "python uphyloplot2.py -c 15" and so on. The default is set to 5 (Only subclones that comprise at least 5% of cells will be included for plotting), so it will filter out some subclones (as we see in our input .cell_groupings file) even if we do not set a threshold ourselves.
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Related Issues (19)
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