Observations (Data points)

In the context of SPATA2, the term observations refers to the data points or entities for which spatial information (x- and y-coordinates) as well as molecular data (e.g. gene expression) and meta data (e.g. cluster assignment) is captured. The term observational unit is the term that best characterizes these data points as a whole. E.g. cells for platform MERFISH, barcoded spots for platform Visium, barcoded beads for platform SlideSeq and so on.

Throughout documentation the term data points and observations are used synonymously. Usually, when data regarding these data points is extracted as with getCoordsDf(), it comes in form of data.frames where each row corresponds to an observation and each column corresponds to a variable of this observation.