# Spatial Overlay for Omic Data from Nanostring GeoMx Data

## Documentation for package ‘SpatialOmicsOverlay’ version 1.4.0

- 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