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cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/
MIT License
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How to extract dimension data after clustering in monocle3 #75

Closed yanhaidong1 closed 3 years ago

yanhaidong1 commented 3 years ago

Hi,

I just updated the cicero from monocle2 to monocle3 and found there are some functions lost. eg. I want to extract dimension using cds@reducedDimA or cds@reducedDimS but these two are disappeared. Where do I find the dimension data after doing the 'reduce_dimension' and 'cluster_cells'? I will to replace them by my own clustering dimension.

Best wishes, Haidong

hpliner commented 3 years ago

Hello, with the new cds functions, you can get the dimension reduction coordinates using "reducedDims(cds)"

yanhaidong1 commented 3 years ago

Got it. Thanks a lot!