Question about Supplementary Figure 7e

[Chuang1118]

Hello CellTrek,

Congratulations for this tools, which seems impressive!
I tried understanding supp.fig-7e,
You've identified the three tumor subclones locations, and five clusters by unsupervised learning, right?
Then, you validate results by G.E. based spearman correlation analysis.
How to create matrix based on clustering? By mean gene expression ? and how to select gene ?
Can you please post the code or pseudo code to this analysis?

Thanks in advance,
Chuang

[WandeRum]

Hi Chuang,
Thank you for asking. You can create a clustering-level gene matrix using the AverageExpression function in Seurat. Gene selection was followed by the usual Seurat analysis pipeline.
Hope this helps!