Comments (1)
Thanks for your interest! So the first plot isn't pruning anything as you did not specify a prune parameter (--smart-cutoff
only statistically decides what the cutoff value should be, not which cutting should be used, such as --min-size
and --min-distance-search
, you can read about it in the paper https://www.nature.com/articles/s41592-020-0748-5). The second plot is just pruning based on the minimum allowed size for a node.
In our own experience, using --smart-cutoff
with --min-distance-search
provides fantastic results, as it statistically searches for heterogeneous populations and collapses homogeneous populations.
from too-many-cells.
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from too-many-cells.