The SpatialMethod - Class — SpatialMethod-class • SPATA2

Defines the core features of spatial biology platforms like Visium and SlideSeq.

Slots

info: list. List of miscellaneous meta data about the method.
method_specific: list. List method specific data. Depending on the method certain slot names are reserved. See section Method specifics: for more information.
name: character. The name of the spatial method. (E.g. 'VisiumSmall', 'VisiumHD', 'MERFISH', ...). Should be one of validSpatialMethods().
observational_unit: character. Name with which to refer to the data points the method focuses on. (E.g. 'barcode_spot', or 'cell')
unit: character. The SI to be used by default.

Method specifics

Slot @method_specific contains a versatile list of information around specific methods. Depending on the type several slots are reserved/should be set:

For methods of type Visium (currently known VisiumSmall and VisiumLarge):

ccd: Center to center distance as a spatial distance measure in SI units.
diameter: Diameter of each spot in micrometer.
fiducial_frame: List of length two, named x and y. Provides standardized measures of the fiducial frame(in SI units).

For methods that of type SlideSeq (currently known SlideSeqV1):

diameter: Diameter of each bead in micrometer.

Distance measures

The vignette on distance measures in SPATA2 has been replaced. Click here to read it.