Spatial Overlay for Omic Data from Nanostring GeoMx Data

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Documentation for package ‘SpatialOmicsOverlay’ version 1.9.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

add4ChannelImage	Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image
addImageFile	Add image to SpatialOverlay from disk
addImageOmeTiff	Add image to SpatialOverlay from OME-TIFF
addPlottingFactor	Add plotting factor to 'SpatialOverlay' object
addPlottingFactor-method	Add plotting factor to 'SpatialOverlay' object
annotMatching	Match ROIs in annotation file to xml
bookendStr	Print long string in more managable fashion
changeColoringIntensity	Update color intensities for changing to RGB image
changeImageColoring	Update color scheme for changing to RGB image
checkValidRes	Determine lowest resolution image in OME-TIFF
class:SpatialOverlay	Class to Contain NanoString Spatial Overlay Images and Data
class:SpatialPosition	Class to Contain NanoString Spatial Overlay ROI information
coords	Class to Contain NanoString Spatial Overlay Images and Data
coords-method	Class to Contain NanoString Spatial Overlay Images and Data
createCoordFile	Create coordinate file for entire scan
createMask	Create a binary mask from a base 64 string
cropSamples	Crop to zoom in on given ROIs
cropTissue	Crop to remove black boundary around tissue.
downloadMouseBrainImage	Download Mouse Brain OME-TIFF from NanoString's Spatial Organ Atlas
flipX	Flip x axis in image and overlay points
flipY	Flip y axis in image and overlay points
fluor	Class to Contain NanoString Spatial Overlay Images and Data
fluor-method	Class to Contain NanoString Spatial Overlay Images and Data
fluorLegend	Add legend of fluorescence targets that make up image
imageInfo	Class to Contain NanoString Spatial Overlay Images and Data
imageInfo-method	Class to Contain NanoString Spatial Overlay Images and Data
labWork	Class to Contain NanoString Spatial Overlay Images and Data
labWork-method	Class to Contain NanoString Spatial Overlay Images and Data
meta	Class to Contain NanoString Spatial Overlay ROI information
meta-method	Class to Contain NanoString Spatial Overlay ROI information
moveCoords	Move coordinates if they don't match image
outline	Class to Contain NanoString Spatial Overlay Images and Data
outline-method	Class to Contain NanoString Spatial Overlay Images and Data
overlay	Class to Contain NanoString Spatial Overlay Images and Data
overlay-method	Class to Contain NanoString Spatial Overlay Images and Data
parseOverlayAttrs	Parse the xml file for AOI attributes in GeoMx images
parseScanMetadata	Parse the xml file for the scan metadata of GeoMx images
plotFactors	Class to Contain NanoString Spatial Overlay Images and Data
plotFactors-method	Class to Contain NanoString Spatial Overlay Images and Data
plotSpatialOverlay	overlay plots
position	Class to Contain NanoString Spatial Overlay ROI information
position-method	Class to Contain NanoString Spatial Overlay ROI information
readLabWorksheet	Read lab worksheet into dataframe of annotations
readSpatialOverlay	Read in 'SpatialOverlay' from tiff file and annotations
recolor	recolor images after changing colors and/or color intensities
removeSample	Remove sample(s) from SpatialOverlay
res	Class to Contain NanoString Spatial Overlay Images and Data
res-method	Class to Contain NanoString Spatial Overlay Images and Data
sampNames	Class to Contain NanoString Spatial Overlay Images and Data
sampNames-method	Class to Contain NanoString Spatial Overlay Images and Data
scaleBarRatio	Class to Contain NanoString Spatial Overlay Images and Data
scaleBarRatio-method	Class to Contain NanoString Spatial Overlay Images and Data
scaled	Class to Contain NanoString Spatial Overlay Images and Data
scaled-method	Class to Contain NanoString Spatial Overlay Images and Data
scanMeta	Class to Contain NanoString Spatial Overlay Images and Data
scanMeta-method	Class to Contain NanoString Spatial Overlay Images and Data
seg	Class to Contain NanoString Spatial Overlay Images and Data
seg-method	Class to Contain NanoString Spatial Overlay Images and Data
show-method	Class to Contain NanoString Spatial Overlay Images and Data
show-method	Class to Contain NanoString Spatial Overlay ROI information
showImage	Class to Contain NanoString Spatial Overlay Images and Data
showImage-method	Class to Contain NanoString Spatial Overlay Images and Data
slideName	Class to Contain NanoString Spatial Overlay Images and Data
slideName-method	Class to Contain NanoString Spatial Overlay Images and Data
SpatialOverlay	Class to Contain NanoString Spatial Overlay Images and Data
SpatialOverlay-class	Class to Contain NanoString Spatial Overlay Images and Data
SpatialOverlay-method	Class to Contain NanoString Spatial Overlay Images and Data
spatialPos	Class to Contain NanoString Spatial Overlay ROI information
spatialPos-method	Class to Contain NanoString Spatial Overlay ROI information
SpatialPosition	Class to Contain NanoString Spatial Overlay ROI information
SpatialPosition-class	Class to Contain NanoString Spatial Overlay ROI information
SpatialPosition-method	Class to Contain NanoString Spatial Overlay ROI information
workflow	Class to Contain NanoString Spatial Overlay Images and Data
workflow-method	Class to Contain NanoString Spatial Overlay Images and Data
xmlExtraction	Extract xml from OME-TIFF