The vesalius_assay class — vesalius_assay-class • vesalius

The vesalius_assay class is the functional unit of vesalius. Each assay is stored within this class and it contains all the required information to run analysis on your assay of choice. In this object, you can find spatial tiles, image embeddings, spatial territories, differentially expressed genes (DEG), count matrices (raw and normalised), microscopy images (if present) and a functional log that lets you see what had been run on this object.

Slots

assay: character assay name
tiles: data.frame containing spatial coordinates and pixels tiles once they have been computed
embeddings: list containing latent space embeddings in the form of data.frames.
active: matrix containing active embedding data
territories: data.frame containing spatial color segments, spatial territories, or layers.
DEG: list of data.frame for each differentially gene expression trial
counts: list that containing count matrices. Raw and normalised will be stored here and named by the normalisation method used.
meta: list containing metadata associated with the assay
cost: list containing cost matrices used for mapping assays
map: data.frame containing mapping results between assays
image: list containing associated microscopy images (NOT implemented)
log: list containing analysis history of the object.