yhr91/GEARS_misc

Reproduce figure 3

subercui opened this issue · 1 comments

subercui commented

Hi, I am trying to reproduce the analysis in figure 3, particularly the UMAPs. Could you let me know how to do it?

Some related questions:

  1. Should I use the script https://github.com/yhr91/gears_misc/blob/main/paper/Fig3_UMAP_predict.py and https://github.com/yhr91/gears_misc/blob/main/paper/Fig3_UMAP_train.py?

  2. It seems the Fig3_UMAP_train.py only saved the model, so how did you generate the embeddings used in figure 3b?

  3. Similarly, what embedding vectors you used to generate figure 3c? Is it related to this line https://github.com/yhr91/gears_misc/blob/73a026049d22107ef1a31c81cb677f646b62dea1/paper/Fig3_UMAP_predict.py#L69

Thank you!

yhr91 commented

Sorry for the late reply, wasn't notified about this issue.

  1. Yes, those were the scripts used to produce the results

  2. I've added the notebook to this repository that was used to generate figure 3

  3. Yes, we used model_name+'_all_preds' to make the UMAP