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rajewsky-lab / novosparc

BSD 3-Clause "New" or "Revised" License
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Can we get the relative distance of all cells? #30

Closed YiweiNiu closed 3 years ago

YiweiNiu commented 4 years ago

Hi,

Thank you for this great package!

I wonder if we could get the relative distance of all cells. If I understand correctly, novoSpaRc returns the expression data on spatial locations, and it may calculate the "physical distance" between cells.

How can we get this information?

Sorry if my question is too naive or due to my ignorance.

Many thanks! Yiwei Niu

nukappa commented 4 years ago

Hi, can you please explain in more detail what you mean by "relative distance of all cells"? novoSpaRc will map the cells spatially and provide the spatial DGE matrix. The "physical distances" between the mapped locations are given, as you provide the target space for the reconstruction.

YiweiNiu commented 4 years ago

Thank you for your reply!

Sorry I did not make myself clear. I mean, for example, for cell A and cell B, can we get the spatial distance between them?

By viewing the final spatial expression of specific marker genes, I could see cells of group A and cells of group B are close. But it is a visual check, what I want to do is to qualify the distances between groups of cells, i.e. to compare if the distance between group A and group B is smaller than that of group A and group C.

Hope that I did not misunderstand the purpose of novosparc.

nukappa commented 4 years ago

Hi, we currently don't have a function that does this, but you can compute it on your own by using the geometrical locations and the final sdge produced with novosparc.