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balicea / DevoWorm

Code for DevoWorm project
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Resolve self-loops in differentiation tree spreadsheet #76

Closed mwatts15 closed 7 years ago

mwatts15 commented 8 years ago

These cells have self-loops in the spreadsheet.

Source
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ABplaappa
ABplappaa
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balicea commented 8 years ago

Mark, Ignore daughter cells with same ID as mother cells (so-called self-loops). Again, ignore the daughters, not the mother cells. They are pretty far down the tree, and got appended as daughters for some reason.

mwatts15 commented 8 years ago

Thanks Bradly. The problem I have is that these nodes are disconnected from P0 in the relative-size graph. I can reconnect based on the lineage name, but when there are two daughters and one has the same ID as the parent, does this mean it's actually an asymmetric division? In that case, what do the relative sizes mean?

balicea commented 8 years ago

Yes, these cells represent asymmetric divisions, and do not have relative sizes. You may exclude them from the relative size graph. Later in the AB lineage (and much sooner in the C, D, and P lineages -- although these cases have been pre-excluded), you get asymmetric divisions either due to cells that finish differentiating or apoptosis (programmed cell death). For our purposes, these cells do not yield any information.