Package: SpatialOmicsOverlay 1.13.0

Maddy Griswold

SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data

Tools for NanoString Technologies GeoMx Technology. Package to easily graph on top of an OME-TIFF image. Plotting annotations can range from tissue segment to gene expression.

Authors:Maddy Griswold [cre, aut], Megan Vandenberg [ctb], Stephanie Zimmerman [ctb]

SpatialOmicsOverlay_1.13.0.tar.gz
SpatialOmicsOverlay_1.13.0.zip(r-4.7)SpatialOmicsOverlay_1.13.0.zip(r-4.6)SpatialOmicsOverlay_1.13.0.zip(r-4.5)
SpatialOmicsOverlay_1.13.0.tgz(r-4.6-any)SpatialOmicsOverlay_1.13.0.tgz(r-4.5-any)
SpatialOmicsOverlay_1.13.0.tar.gz(r-4.7-any)SpatialOmicsOverlay_1.13.0.tar.gz(r-4.6-any)
SpatialOmicsOverlay_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
SpatialOmicsOverlay/json (API)
NEWS

# Install 'SpatialOmicsOverlay' in R:
install.packages('SpatialOmicsOverlay', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:SpatialOmicsOverlay-1.13.0(bioc 3.24)SpatialOmicsOverlay-1.12.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressiontranscriptioncellbasedassaysdataimporttranscriptomicsproteomicsproprietaryplatformsrnaseqspatialdatarepresentationvisualizationopenjdk

4.72 score 21 scripts 256 downloads 47 exports 149 dependencies

Last updated from:840708e9cb. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING240
linux-devel-x86_64WARNING954
source / vignettesOK984
linux-release-x86_64WARNING801
macos-release-arm64WARNING670
macos-oldrel-arm64WARNING682
windows-develWARNING1095
windows-releaseWARNING1017
windows-oldrelWARNING1033
wasm-releaseOK209

Exports:add4ChannelImageaddImageFileaddImageOmeTiffaddPlottingFactorbookendStrchangeColoringIntensitychangeImageColoringcheckValidRescoordscreateCoordFilecreateMaskcropSamplescropTissuedownloadMouseBrainImageflipXflipYfluorfluorLegendimageInfolabWorkmetamoveCoordsoutlineoverlayparseOverlayAttrsparseScanMetadataplotFactorsplotSpatialOverlaypositionreadLabWorksheetreadSpatialOverlayrecolorremoveSampleressampNamesscaleBarRatioscaledscanMetasegshowshowImageslideNameSpatialOverlayspatialPosSpatialPositionworkflowxmlExtraction

Dependencies:abindaskpassbase64encbeeswarmBiobaseBiocFileCacheBiocGenericsBiostringsbitbit64bitopsblobbootbslibcachemcellrangerclicodetoolscommonmarkcpp11crayoncurldata.tableDBIdbplyrdigestdotCall64dplyrEBImageEnvStatsevaluatefarverfastmapfftwtoolsfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforcatsfsfuturefuture.applygdtoolsgenericsGeomxToolsGGallyggbeeswarmggiraphggplot2ggstatsggtextggthemesglobalsgluegridtextgtablehighrhmshtmltoolshtmlwidgetshttr2IRangesisobandjpegjquerylibjsonliteknitrlabelinglatticelifecyclelistenvlitedownlme4lmerTestlocfitmagickmagrittrmarkdownMASSMatrixmemoisemimeminqaNanoStringNCToolsnlmenloptrnortestnumDerivopensslparallellypatchworkpbapplypheatmappillarpkgconfigplotrixplyrpngprettyunitsprogressprogressrpurrrR6rappdirsrbibutilsRBioFormatsRColorBrewerRcppRcppEigenRCurlRdpackreadxlreformulasrematchreshape2rJavarjsonrlangrmarkdownRSQLiteS4VectorsS7sassscalesscattermoreSeqinfoSeuratObjectspspamstringistringrsyssystemfontstibbletidyrtidyselecttifftinytexutf8vctrsviporviridisLitewithrxfunXMLxml2XVectoryaml

Introduction to SpatialOmicsOverlay

Rendered fromSpatialOmicsOverlay.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-05-12
Started: 2022-03-31

Readme and manuals

Help Manual

Help pageTopics
Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of imageadd4ChannelImage
Add image to SpatialOverlay from diskaddImageFile
Add image to SpatialOverlay from OME-TIFFaddImageOmeTiff
Add plotting factor to 'SpatialOverlay' objectaddPlottingFactor addPlottingFactor,character-method addPlottingFactor,data.frame-method addPlottingFactor,factor-method addPlottingFactor,matrix-method addPlottingFactor,NanoStringGeoMxSet-method addPlottingFactor,numeric-method addPlottingFactor,tbl-method addPlottingFactor,tbl_df-method
Match ROIs in annotation file to xmlannotMatching
Print long string in more managable fashionbookendStr
Update color intensities for changing to RGB imagechangeColoringIntensity
Update color scheme for changing to RGB imagechangeImageColoring
Determine lowest resolution image in OME-TIFFcheckValidRes
Create coordinate file for entire scancreateCoordFile
Create a binary mask from a base 64 stringcreateMask
Crop to zoom in on given ROIscropSamples
Crop to remove black boundary around tissue.cropTissue
Download Mouse Brain OME-TIFF from NanoString's Spatial Organ AtlasdownloadMouseBrainImage
Flip x axis in image and overlay pointsflipX
Flip y axis in image and overlay pointsflipY
Add legend of fluorescence targets that make up imagefluorLegend
Move coordinates if they don't match imagemoveCoords
Parse the xml file for AOI attributes in GeoMx imagesparseOverlayAttrs
Parse the xml file for the scan metadata of GeoMx imagesparseScanMetadata
overlay plotsplotSpatialOverlay
Read lab worksheet into dataframe of annotationsreadLabWorksheet
Read in 'SpatialOverlay' from tiff file and annotationsreadSpatialOverlay
recolor images after changing colors and/or color intensitiesrecolor
Remove sample(s) from SpatialOverlayremoveSample
Class to Contain NanoString Spatial Overlay Images and Dataclass:SpatialOverlay coords coords,SpatialOverlay-method fluor fluor,SpatialOverlay-method imageInfo imageInfo,SpatialOverlay-method labWork labWork,SpatialOverlay-method outline outline,SpatialOverlay-method overlay overlay,SpatialOverlay-method plotFactors plotFactors,SpatialOverlay-method res res,SpatialOverlay-method sampNames sampNames,SpatialOverlay-method scaleBarRatio scaleBarRatio,SpatialOverlay-method scaled scaled,SpatialOverlay-method scanMeta scanMeta,SpatialOverlay-method seg seg,SpatialOverlay-method show,SpatialOverlay-method showImage showImage,SpatialOverlay-method slideName slideName,SpatialOverlay-method SpatialOverlay SpatialOverlay,character-method SpatialOverlay-class workflow workflow,SpatialOverlay-method
Class to Contain NanoString Spatial Overlay ROI informationclass:SpatialPosition meta meta,SpatialPosition-method position position,SpatialPosition-method show,SpatialPosition-method spatialPos spatialPos,SpatialPosition-method SpatialPosition SpatialPosition,data.frame-method SpatialPosition,environment-method SpatialPosition,matrix-method SpatialPosition,missing-method SpatialPosition-class
Extract xml from OME-TIFFxmlExtraction