SpatialMethod-class: The 'SpatialMethod' - Class

In kueckelj/SPATA2: A Toolbox for Spatial Expression Analysis

The SpatialMethod - Class

Description

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.

kueckelj/SPATA2 documentation built on Feb. 27, 2025, 1:45 p.m.