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

View source: R/xmlParsing.R

parseOverlayAttrsR Documentation

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 April 20, 2024, 5:36 a.m.