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TrigosTeam / SPIAT

https://trigosteam.github.io/SPIAT/
Artistic License 2.0
21 stars 8 forks source link

Importing annotation and specifying exclusion (negative) markers #23

Closed prestigious-bat3868 closed 1 year ago

prestigious-bat3868 commented 1 year ago

First of all, this is an amazing package, kudos. I have two questions:

  1. Is there any way to import annotations (eg from HALO) to calculate the frequency of cells within manually annotated regions (eg tumour vs non-tumour)? The automatic identification of tumour structure function in SPIAT doesn't work well for my tissue (brain).

If no such way currently exists, do you have any thoughts about a potential workaround?

  1. How can I define a negative marker in my phenotype, e.g. "CD4+ PD1-"? I presume "CD4" just means "CD4" regardless of PD1 status.

Thank you in advance!

fuerzhou commented 1 year ago

Thanks for your interest in the tool.

  1. The package doesn't support importing the annotations directly. A workaround would be manually adding a column to the colData() of the SpatialExperiment Object. You need to make sure the cell IDs match the corresponding annotations.
  2. "CD4" means there is only "CD4" present on the cell without other markers. Cheers, Yuzhou
prestigious-bat3868 commented 1 year ago

Thank you!