mapSpatialAnnotationTags: Spatial annotation and barcode intersection
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

mapSpatialAnnotationTags

R Documentation

Spatial annotation and barcode intersection

Description

Creates a data.frame that maps the tags of spatial annotations to the barcodes that were covered by the spatial extent of the respective spatial annotation.

Usage

mapSpatialAnnotationTags(
  object,
  ids = NULL,
  tags = NULL,
  merge = TRUE,
  merge_name = "spat_annotations",
  merge_missing = "none",
  merge_sep = "_",
  merge_drop = FALSE
)

Arguments

`object`	An object of class `SPATA2` or, in case of S4 generics, objects of classes for which a method has been defined.
`tags`	Character vector or `NULL`. If character, the tags for the image annotation selection. See section Selection of spatial annotations for more information.
`merge`	Logical value. If TRUE, the results are merged in a single variable.
`merge_name`	Character value. The name of the merged variable.
`merge_missing`	Character value. The value that is assigned to barcodes that do not fall in the extent of any image annotation.
`merge_sep`	Character value. The string with which the image annotation tags are separated with while being merged.
`merge_drop`	Logical value. If TRUE and `merge` is TRUE, all image-annotation- tag-variables are dropped.