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Selection of distinct peak locations for negative binomial simulations #3

Open aplazar1 opened 7 months ago

aplazar1 commented 7 months ago

Hello! I was trying to reproduce your Tricycle paper SI results (Universal prediction of cell cycle position using transfer learning)...particularly, the negative binomial simulations in SI Figs S1-S3, but it seems like the spheroid shape may be not only dependent upon the number of peaks but also their location. Could you please explain how you selected the distinct peak locations? Did you sample them from a distribution? Many Thanks!

kasperdanielhansen commented 7 months ago

We sample them and I believe the code is in the paper repository. Have you looked?

On Wed, Jan 24, 2024 at 3:07 PM aplazar1 @.***> wrote:

Hello! I was trying to reproduce your Tricycle paper SI results (Universal prediction of cell cycle position using transfer learning)...particularly, the negative binomial simulations in SI Figs S1-S3, but it seems like the spheroid shape may be not only dependent upon the number of peaks but also their location. Could you please explain how you selected the distinct peak locations? Did you sample them from a distribution? Many Thanks!

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aplazar1 commented 7 months ago

Hi! Good morning! I had looked in the tricycle_paper_figs/scripts/figs/response.2peaksloc.R but was having trouble finding it. Thanks for your prompt response!

aplazar1 commented 7 months ago

I understand that theta is sampled from a uniform distribution, but what I don't quite understand is how Lg is selected from the methods description. I am referring to the equation lambda_g = A_g cos(theta-Lg) from the methods section. Many Thanks!