How to incorporate additional covariate matrices

[bmill3r]

Hello,

Thanks so much for this great tool!

I am interested in applying SPARK-X to some large spatial datasets and would also like to incorporate additional covariate matrices, such as cell type compositions as spatial locations, into the model.

In the paper, cell type compositions were used as covariates for analysis of the Slide-seqV2 and HDST datasets. Could you provide more information on how to construct these covariate matrices and input them into SPARK-X? On the Examples page, I see an option to add a covariate matrix for SPARK, but not for SPARK-X. Also, there are no instructions as to how this matrix should be structured. Could you please provide more context or an example?

Thank you, Brendan