Platform dependent input recommendations

A collection of functions that return the recommended default input of certain arguments depending on the spatial method (the platform) the SPATA2 object derived from.

recAlpha(object)

recDbscanEps(object)

recDbscanMinPts(object)

recSgsRes(object, unit = getDefaultUnit(object))

Arguments

object

An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.

unit

Character value. Specifies the desired unit in which distance measures or area measures are provided. Run validUnitsOfLength() or validUnitsOfArea() for valid input options.

Value

Single values of different classes depending on the function. See details for more.

Details

  • recAlpha The recommended alpha input for alphahull::ahull(). For objects derived from the Visium platform, we recommend a binwidth equal to the center-to-center distance as obtained by getCCD() multiplied by 1.25. For objects derived from platforms that do not rely on a fixed grid of data points (MERFISH, SlideSeq, etc.), we recommend the average minimal distance between the data points multiplied by 1.25.

  • recDbscanEps The default input for the eps argument of dbscan::dbscan(). For objects derived from the Visium platform, we recommend a binwidth equal to the center-to-center distance as obtained by getCCD() multiplied by 1.25. For objects derived from platforms that do not rely on a fixed grid of data points (MERFISH, SlideSeq, etc.), we recommend the average minimal distance between the data points multiplied by 1.25.

  • recDbscanMinPts The default input for the minPts argument of dbscan::dbscan(). For objects derived from the Visium platform, we recommend minPts = 3. For objects derived from platforms that do not rely on a fixed grid of data points (MERFISH, SlideSeq, etc.), we recommend minPts = 12.

  • recSgsRes() The default input for the resolution argument of the spatial gradient screening algorithm. For objects derived from the Visium platform, we recommend a binwidth equal to the center-to-center distance as obtained by getCCD(). For objects derived from platforms that do not rely on a fixed grid of data points (MERFISH, SlideSeq, etc.), we recommend the average minimal distance between the data points.