addMoleculeCoordinates: Add molecule coordinates

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Add molecule coordinates

Description

Adds or updates the molecule coordinates for a specified assay in the given object.

Usage

addMoleculeCoordinates(
  object,
  coordinates = NULL,
  assay_name = activeAssay(object)
)

Arguments

object	An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
coordinates	A data frame containing the coordinates to be added. The data frame must contain the following variables: molecule or <assay_name> Identifier for the molecules. E.g. if x_orig or x: x-coordinates (original or to be scaled back to original). y_orig or y: y-coordinates (original or to be scaled back to original).
assay_name	Only relevant if the SPATA2 object contains more than one assay: Denotes the assay of interest and thus the molecular modality to use. Defaults to the active assay as set by activateAssay().

Details

This function processes the provided coordinates data frame to ensure it contains the necessary variables (molecule or the assay name, x or x_orig, and y or y_orig). If only the scaled coordinates (x and y) are provided, they are scaled back to the original coordinate frame using the image scale factor. The resulting data frame is then nested by the assay modality and integrated into the molecular metadata variables of the object.

Results are stored in a nested column in the molecular meta variable data.frame called coords.

Value

The updated input object, containing the added, removed or computed results.

See Also

getMolecularCoordinates(), getMetaVarDf()

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.