how to generate figure like this

kstreet13 / bioc2020trajectories

Trajectory inference and differential expression over multiple conditions in scRNA-seq

https://kstreet13.github.io/bioc2020trajectories/

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how to generate figure like this #2

Closed FADHLyemen closed 2 years ago

FADHLyemen commented 2 years ago

Hi @kstreet13, I am trying to plot a similar figure like your: is it a umap for your cells colored by your conditions? What kind of dimensionality reduction you use. do you have the code to produce it?

kstreet13 commented 2 years ago

Hi @FADHLyemen ,

This figure is from the condiments paper and all the code can be found here: https://github.com/HectorRDB/condimentsPaper.

I don't know for certain what type of dimensionality reduction was used, but it is colored by condition, yes. However, this is simulated data, so whatever dimensionality reduction was used, this result is likely much cleaner than anything you would see with real data.