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✨
DESCRIPTION |NEWS
card.svg |card.png
SpatialOmicsOverlay/json (API)

# 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.

geneexpression transcription cellbasedassays dataimport transcriptomics proteomics proprietaryplatforms rnaseq spatial datarepresentation visualization openjdk

4.63 score 17 scripts 47 exports 149 dependencies

Last updated from:840708e9cb. Checks:6 WARNING, 2 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	261
linux-devel-x86_64	ERROR	826
source / vignettes	OK	896
linux-release-x86_64	WARNING	968
macos-release-arm64	WARNING	601
macos-oldrel-arm64	WARNING	625
windows-devel	ERROR	999
windows-release	WARNING	1105
windows-oldrel	WARNING	1335
wasm-release	OK	244

Exports:add4ChannelImage addImageFile addImageOmeTiff addPlottingFactor bookendStr changeColoringIntensity changeImageColoring checkValidRes coords createCoordFile createMask cropSamples cropTissue downloadMouseBrainImage flipX flipY fluor fluorLegend imageInfo labWork meta moveCoords outline overlay parseOverlayAttrs parseScanMetadata plotFactors plotSpatialOverlay position readLabWorksheet readSpatialOverlay recolor removeSample res sampNames scaleBarRatio scaled scanMeta seg show showImage slideName SpatialOverlay spatialPos SpatialPosition workflow xmlExtraction

Dependencies:abind askpass base64enc beeswarm Biobase BiocFileCache BiocGenerics Biostrings bit bit64 bitops blob boot bslib cachem cellranger cli codetools commonmark cpp11 crayon curl data.table DBI dbplyr digest dotCall64 dplyr EBImage EnvStats evaluate farver fastmap fftwtools filelock fontawesome fontBitstreamVera fontLiberation fontquiver forcats fs future future.apply gdtools generics GeomxTools GGally ggbeeswarm ggiraph ggplot2 ggstats ggtext ggthemes globals glue gridtext gtable highr hms htmltools htmlwidgets httr2 IRanges isoband jpeg jquerylib jsonlite knitr labeling lattice lifecycle listenv litedown lme4 lmerTest locfit magick magrittr markdown MASS Matrix memoise mime minqa NanoStringNCTools nlme nloptr nortest numDeriv openssl parallelly patchwork pbapply pheatmap pillar pkgconfig plotrix plyr png prettyunits progress progressr purrr R6 rappdirs rbibutils RBioFormats RColorBrewer Rcpp RcppEigen RCurl Rdpack readxl reformulas rematch reshape2 rJava rjson rlang rmarkdown RSQLite S4Vectors S7 sass scales scattermore Seqinfo SeuratObject sp spam stringi stringr sys systemfonts tibble tidyr tidyselect tiff tinytex utf8 vctrs vipor viridisLite withr xfun XML xml2 XVector yaml

Introduction to SpatialOmicsOverlay

Rendered fromSpatialOmicsOverlay.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

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