Molecular Modalities

SPATA2 was developed with the Visium platform in mind which revolves around spatial gene expression. With SPATA2 v3.0.0 we aim to expand the package to include different platforms and more molecular modalities to analyze spatial distribution of proteins or metabolites, too. Hence, when creating objects with molecular assays the modality must be specified.

To ensure that inbuilt functions of SPATA2 like gene set enrichment or copy number variation analysis work seamlessly, the modality must be specified "correctly".

SPATA2 knows three molecular modalities for which specific functions have been written like the ones linked above.

  1. Gene expression: Use modality = 'gene'

  2. Protein expression: Use modality = 'protein'

  3. Metabolites expression: Use modality = 'metabolite'

Depending on the modality of an assay, specific functions can be used or not. For instance, runCNV() only works if SPATA2 object contains an assay of data modality gene (not genes, rna, mRNA or anything else). This extends to the inbuilt concept of molecular signatures. It is not forbidden, of course, to create molecular assays with modalities differing from the ones SPATA2 knows. It is just that you won't be able to use certain functions with the created assay.

Molecular Modality == Assay Name!

The molecular modality of an assay also defines its name! Hence, if you encounter the parameter assay_name it can be thought of defining the molecular modality of interest! And the output of activeAssay() can be thought of the output of active molecular modality.