parseOverlayAttrs: Parse the xml file for AOI attributes in GeoMx images

In Nanostring-Biostats/SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data

Parse the xml file for AOI attributes in GeoMx images

Description

Parse the xml file for AOI attributes in GeoMx images

Usage

parseOverlayAttrs(omexml, annots, labworksheet, ...)

Arguments

omexml	xml file from OME-TIFF, can provide path to OME-TIFF and xml will automatically be extracted
annots	df of annotations
labworksheet	annots are from lab worksheet file
...	segCol in annotMatching, if auto detection doesn't work.

Value

SpatialPosition of AOIs containing metadata and base64encoded positions

Examples

image <- downloadMouseBrainImage()

xml <- xmlExtraction(ometiff = image)

muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

overlay <- parseOverlayAttrs(omexml = xml, 
                             annots = muBrainLW, 
                             labworksheet = TRUE)

Nanostring-Biostats/SpatialOmicsOverlay documentation built on Dec. 18, 2024, 9:26 a.m.