How to get the cell-cell similarity matrix from secedo?

[jingliulj]

Hi,

I get the eigenvectors&values from secedo and all the cluster_*.vcf files (why there are many empty clusters?), but cannot find the similarity matrix as mentioned in the preprint paper. Can you help with this? Thanks!

Jing

[danieldanciu]

You need to change the source code to print the entire matrix. At the following line: https://github.com/ratschlab/secedo/blob/f5944261e21815b7d2862b0a501e205b0ff71a93/spectral_clustering.cpp#L357 insert something like: std::ofstream f(out_dir + marker); f << sim_mat; f.close(); then recompile Secedo and you'll get the similarity matrix logged.

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On Wed, 25 May 2022 at 09:30, Jing LIU ***@***.***> wrote: Hi, I get the eigenvectors&values from secedo and all the cluster_*.vcf files, but cannot find the similarity matrix as mentioned in the preprint paper. Can you help with this? Thanks! Jing — Reply to this email directly, view it on GitHub <#20>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAOYQLFHIMSZXXIPRYRPM3DVLXJI7ANCNFSM5W4EEKDQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>