Comments (4)
Hi,
What do you mean by "what are the cells"?, do you mean how you get their barcode? or how you visualize them?
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Hello,
I want get their barcode.I'm not trying to visualize them. I need to know the specific cells of each lineage (barcode), such as 6-5(0.86), 5-3(0.82).
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Please use aggregation_mode="cell"
, and source_groups=None
in cell_transition
.
This gives you a map from each single cell to a cluster. Then you can identify for each single cell what the most likely cluster is and thus select all cells in the source distribution which are most likely mapped to cluster 5.
@ArinaDanilina I just realized we don't have an example for this, could you please add the aggregation_mode="cell"
to the cell transition example and keep @dawangran updated? https://moscot.readthedocs.io/en/latest/notebooks/examples/plotting/200_cell_transitions.html
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Hi @dawangran ,
You might have noticed that we added an example here: https://moscot.readthedocs.io/en/latest/notebooks/examples/plotting/200_cell_transitions.html
I am closing this for now, please feel free to reopen if you have more questions.
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Related Issues (20)
- test_fgw_problem.py: test_prepare_costs alpha given to prepare HOT 1
- Buggy Test: test_gw_problem gives joint_attr HOT 1
- Buggy Test: `scale_cost` given to prepare in tests/problems/time/test_mixins.py HOT 1
- check the convergence flag
- change links to papers
- adapt low rank gamma default for linear problems HOT 1
- describe birth death process better HOT 1
- adapt user guide
- Refactor: Check if both x and x_callback is given
- Refactor: Maybe GW should inherit from FGW instead of vice versa HOT 2
- check for failing tests HOT 1
- check for unrecognized in `solve` methods
- check for warnings thrown by us
- Add Elastic Costs again or asses if they are necessary or not HOT 2
- Plotting Tests Fail HOT 1
- `.impute` consumes too much memory HOT 2
- output the raw cell transition data without aggregation HOT 6
- Full rank initializers
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