Package 'SpatialOmicsOverlay' reference manual

Title:	Spatial Overlay for Omic Data from Nanostring GeoMx Data
Description:	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]
Maintainer:	Maddy Griswold <[email protected]>
License:	MIT
Version:	1.5.0
Built:	2024-07-20 05:37:37 UTC
Source:	https://github.com/bioc/SpatialOmicsOverlay

Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image

Description

Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image

Usage

add4ChannelImage(overlay, ometiff = NULL, res = NULL, ...)
add4ChannelImage(overlay, ometiff = NULL, res = NULL, ...)

Arguments

`overlay`	SpatialOverlay object
`ometiff`	File path to OME-TIFF. NULL indicates pull info from overlay
`res`	resolution layer, 1 = largest & higher values = smaller. The images increase in resolution and memory. The largest image your environment can hold is recommended. NULL indicates pull info from overlay
`...`	Extra variables

Value

SpatialOverlay object with image

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

dim(EBImage::imageData(showImage(muBrain)))

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

dim(EBImage::imageData(showImage(muBrain)))

Add image to SpatialOverlay from disk

Description

Add image to SpatialOverlay from disk

Usage

addImageFile(overlay, imageFile = NULL, res = NULL)
addImageFile(overlay, imageFile = NULL, res = NULL)

Arguments

`overlay`	SpatialOverlay object
`imageFile`	path to image
`res`	what resolution is the image given? 1 = largest, higher number = smaller This value will affect the coordinates of the overlays. res = 2, resolution is 1/2 the size as the raw image res = 3, resolution is 1/4 the size as the raw image res = 4, resolution is 1/8 the size as the raw image resolution = 1/2^(res-1)

Value

SpatialOverlay object with image

Add image to SpatialOverlay from OME-TIFF

Description

Add image to SpatialOverlay from OME-TIFF

Usage

addImageOmeTiff(overlay, ometiff = NULL, res = NULL, ...)
addImageOmeTiff(overlay, ometiff = NULL, res = NULL, ...)

Arguments

`overlay`	SpatialOverlay object
`ometiff`	File path to OME-TIFF. NULL indicates pull info from overlay
`res`	resolution layer, 1 = largest & higher values = smaller. The images increase in resolution and memory. The largest image your environment can hold is recommended. NULL indicates pull info from overlay
`...`	Extra variables

Value

SpatialOverlay object with image

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)
showImage(muBrain)

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)
showImage(muBrain)

Add plotting factor to `SpatialOverlay` object

Description

Add plotting factor to SpatialOverlay object

Usage

addPlottingFactor(overlay, annots, plottingFactor, ...)

## S4 method for signature 'NanoStringGeoMxSet'
addPlottingFactor(overlay, annots, plottingFactor, countMatrix = "exprs")

## S4 method for signature 'matrix'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'tbl_df'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'tbl'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'data.frame'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'character'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'numeric'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'factor'
addPlottingFactor(overlay, annots, plottingFactor)
addPlottingFactor(overlay, annots, plottingFactor, ...)

## S4 method for signature 'NanoStringGeoMxSet'
addPlottingFactor(overlay, annots, plottingFactor, countMatrix = "exprs")

## S4 method for signature 'matrix'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'tbl_df'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'tbl'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'data.frame'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'character'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'numeric'
addPlottingFactor(overlay, annots, plottingFactor)

## S4 method for signature 'factor'
addPlottingFactor(overlay, annots, plottingFactor)

Arguments

`overlay`	`SpatialOverlay` object
`annots`	factor vector with the plottingFactor. if names match sample names in overlay vector will be matched on those, otherwise assumed in the correct order
`plottingFactor`	name of the new plotting factor
`...`	if using `NanoStringGeoMxSet`, name of count matrix to pull counts from
`countMatrix`	name of count matrix to pull counts from

Value

SpatialOverlay object with new plotting factor

Examples

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

muBrain <- addPlottingFactor(overlay = muBrain, 
                             annots = muBrainLW, 
                             plottingFactor = "segment")

muBrainGxT <- readRDS(unzip(system.file("extdata", "muBrain_GxT.zip", 
                                  package = "SpatialOmicsOverlay")))

muBrain <- addPlottingFactor(overlay = muBrain, 
                             annots = muBrainGxT, 
                             plottingFactor = "Calm1",
                             countMatrix = "exprs")

muBrain <- addPlottingFactor(overlay = muBrain,
                             annots = seq_len(length(sampNames(muBrain))),
                             plottingFactor = "ROINum")

head(plotFactors(muBrain))

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrain <- addPlottingFactor(overlay = muBrain,
                             annots = as.factor(seq_len(length(sampNames(muBrain)))),
                             plottingFactor = "ROINum")

head(plotFactors(muBrain))
muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

muBrain <- addPlottingFactor(overlay = muBrain, 
                             annots = muBrainLW, 
                             plottingFactor = "segment")

muBrainGxT <- readRDS(unzip(system.file("extdata", "muBrain_GxT.zip", 
                                  package = "SpatialOmicsOverlay")))

muBrain <- addPlottingFactor(overlay = muBrain, 
                             annots = muBrainGxT, 
                             plottingFactor = "Calm1",
                             countMatrix = "exprs")

muBrain <- addPlottingFactor(overlay = muBrain,
                             annots = seq_len(length(sampNames(muBrain))),
                             plottingFactor = "ROINum")

head(plotFactors(muBrain))

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrain <- addPlottingFactor(overlay = muBrain,
                             annots = as.factor(seq_len(length(sampNames(muBrain)))),
                             plottingFactor = "ROINum")

head(plotFactors(muBrain))

Match ROIs in annotation file to xml

Description

Match ROIs in annotation file to xml

Usage

annotMatching(annots, ROInum, maskNum, maskText, segCol = NULL)
annotMatching(annots, ROInum, maskNum, maskText, segCol = NULL)

Arguments

`annots`	df of annotations
`ROInum`	ROI number from xml file
`maskNum`	number of masks for ROI, used for AOI matching in software <= v2.4
`maskText`	segment name, used for AOI matching in software v2.4+
`segCol`	column containing segment name, if NULL function will determine automatically

Value

df with ROI unique identifiers

Print long string in more managable fashion

Description

Print first and last n characters of string in this format: "### ... ### (x total char)"

Usage

bookendStr(x, bookend = 8)
bookendStr(x, bookend = 8)

Arguments

`x`	long string
`bookend`	number of characters on either side to print

Value

reformatted string

Examples


start_string <- stringi::stri_rand_strings(n = 1, length = 250)
bookendStr(start_string, bookend = 6)

start_string <- stringi::stri_rand_strings(n = 1, length = 250)
bookendStr(start_string, bookend = 6)

Update color intensities for changing to RGB image

Description

Update color intensities for changing to RGB image

Usage

changeColoringIntensity(overlay, minInten = NULL, maxInten = NULL, dye)
changeColoringIntensity(overlay, minInten = NULL, maxInten = NULL, dye)

Arguments

`overlay`	SpatialOverlay object
`minInten`	value to change MinIntensity to; NULL indicates no change
`maxInten`	value to change MaxIntensity to; NULL indicates no change
`dye`	which dye to change color, can be from Dye or DisplayName column from fluor(overlay)

Value

SpatialOverlay object with updated fluor data

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

fluor(muBrain)

muBrain <- changeColoringIntensity(overlay = muBrain, 
                                   minInten = 500, 
                                   maxInten = 10000, 
                                   dye = "Cy5")

fluor(muBrain)

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

fluor(muBrain)

muBrain <- changeColoringIntensity(overlay = muBrain, 
                                   minInten = 500, 
                                   maxInten = 10000, 
                                   dye = "Cy5")

fluor(muBrain)

Update color scheme for changing to RGB image

Description

Update color scheme for changing to RGB image

Usage

changeImageColoring(overlay, color, dye)
changeImageColoring(overlay, color, dye)

Arguments

`overlay`	SpatialOverlay object, with 4channel image
`color`	color to change dye to, hex or color name
`dye`	which dye to change color, can be from Dye or DisplayName column from fluor(overlay)

Value

SpatialOverlay object with updated fluor data

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = downloadMouseBrainImage(), res = 8)

fluor(muBrain)

muBrain <- changeImageColoring(overlay = muBrain, color = "magenta", 
                               dye = "Cy5")
muBrain <- changeImageColoring(overlay = muBrain, color = "#42f5ef", 
                               dye = "Alexa 488")

fluor(muBrain)

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = downloadMouseBrainImage(), res = 8)

fluor(muBrain)

muBrain <- changeImageColoring(overlay = muBrain, color = "magenta", 
                               dye = "Cy5")
muBrain <- changeImageColoring(overlay = muBrain, color = "#42f5ef", 
                               dye = "Alexa 488")

fluor(muBrain)

Determine lowest resolution image in OME-TIFF

Description

Determine lowest resolution image in OME-TIFF

Usage

checkValidRes(ometiff)
checkValidRes(ometiff)

Arguments

ometiff

path to OME-TIFF

Value

value of lowest res image

Examples


image <- downloadMouseBrainImage()
checkValidRes(ometiff = image)

image <- downloadMouseBrainImage()
checkValidRes(ometiff = image)

Create coordinate file for entire scan

Description

Create coordinate file for entire scan

Usage

createCoordFile(overlay, outline = TRUE)
createCoordFile(overlay, outline = TRUE)

Arguments

`overlay`	SpatialOverlay object
`outline`	returned coordinates only contain boundaries, will not work for segmented ROIs

Value

df of coordinates for every AOI in the scan

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrain <- createCoordFile(muBrain, outline = FALSE)

head(coords(muBrain))

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrain <- createCoordFile(muBrain, outline = FALSE)

head(coords(muBrain))

Create a binary mask from a base 64 string

Description

Create a binary mask from a base 64 string

Usage

createMask(b64string, metadata, outline = TRUE)
createMask(b64string, metadata, outline = TRUE)

Arguments

`b64string`	base 64 string
`metadata`	metadata of AOI including: Height, Width of AOI
`outline`	only the outline points should be returned

Value

binary mask image

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

samp <- which(sampNames(muBrain) == "DSP-1012999073013-A-F12")

ROIMask <- createMask(b64string = position(overlay(muBrain))[samp], 
                      metadata = meta(overlay(muBrain))[samp,],
                      outline = TRUE)

pheatmap::pheatmap(ROIMask, cluster_rows = FALSE, cluster_cols = FALSE)

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

samp <- which(sampNames(muBrain) == "DSP-1012999073013-A-F12")

ROIMask <- createMask(b64string = position(overlay(muBrain))[samp], 
                      metadata = meta(overlay(muBrain))[samp,],
                      outline = TRUE)

pheatmap::pheatmap(ROIMask, cluster_rows = FALSE, cluster_cols = FALSE)

Crop to zoom in on given ROIs

Description

Crop to zoom in on given ROIs

Usage

cropSamples(overlay, sampleIDs, buffer = 0.1, sampsOnly = TRUE)
cropSamples(overlay, sampleIDs, buffer = 0.1, sampsOnly = TRUE)

Arguments

`overlay`	SpatialOverlay object
`sampleIDs`	sampleIDs of ROIs to keep in image
`buffer`	percent of new image size to add to each edge as a buffer
`sampsOnly`	should only ROIs with given sampleIDs be in image

Value

SpatialOverlay object

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

samps <- sampNames(muBrain)

muBrainCrop <- suppressWarnings(cropSamples(overlay = muBrain, 
                                            sampleIDs = samps, 
                                            sampsOnly = TRUE))

plotSpatialOverlay(overlay = muBrainCrop, scaleBar = FALSE,
                   hiRes = TRUE, legend = FALSE)

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

samps <- sampNames(muBrain)

muBrainCrop <- suppressWarnings(cropSamples(overlay = muBrain, 
                                            sampleIDs = samps, 
                                            sampsOnly = TRUE))

plotSpatialOverlay(overlay = muBrainCrop, scaleBar = FALSE,
                   hiRes = TRUE, legend = FALSE)

Crop to remove black boundary around tissue.

Description

Crop to remove black boundary around tissue.

Usage

cropTissue(overlay, buffer = 0.05)
cropTissue(overlay, buffer = 0.05)

Arguments

`overlay`	SpatialOverlay object
`buffer`	percent of new image size to add to each edge as a buffer

Value

SpatialOverlay object

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

muBrainCrop <- cropTissue(overlay = muBrain)

plotSpatialOverlay(overlay = muBrainCrop, legend = FALSE, 
                   hiRes = FALSE, scaleBar = FALSE)
            
muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

muBrainCrop <- cropTissue(overlay = muBrain)

plotSpatialOverlay(overlay = muBrainCrop, legend = FALSE, 
                   hiRes = FALSE, scaleBar = FALSE)

Download Mouse Brain OME-TIFF from NanoString's Spatial Organ Atlas

Description

Download Mouse Brain OME-TIFF from NanoString's Spatial Organ Atlas

Usage

downloadMouseBrainImage()
downloadMouseBrainImage()

Details

https://nanostring.com/products/geomx-digital-spatial-profiler/spatial-organ-atlas/mouse-brain/

Value

mouse brain OME-TIFF

Examples


image <- downloadMouseBrainImage()

image <- downloadMouseBrainImage()

Flip x axis in image and overlay points

Description

Flip x axis in image and overlay points

Usage

flipX(overlay)
flipX(overlay)

Arguments

overlay

SpatialOverlay object

Value

SpatialOverlay object with x axis flipped

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

showImage(flipX(muBrain))

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

showImage(flipX(muBrain))

Flip y axis in image and overlay points

Description

Flip y axis in image and overlay points

Usage

flipY(overlay)
flipY(overlay)

Arguments

overlay

SpatialOverlay object

Value

SpatialOverlay object with y axis flipped

Examples

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

showImage(flipY(muBrain))

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- addImageOmeTiff(overlay = muBrain, 
                           ometiff = image, res = 8)

showImage(flipY(muBrain))

Add legend of fluorescence targets that make up image

Description

Creates legend that can be overlayed on image using cowplot.

Usage

fluorLegend(overlay, nrow = 4, textSize = 10, boxColor = "grey", alpha = 0.25)
fluorLegend(overlay, nrow = 4, textSize = 10, boxColor = "grey", alpha = 0.25)

Arguments

`overlay`	SpatialOverlay
`nrow`	number of rows in the legend. Most studies have 4 which is where the values came from: 1 = horizontal legend, 4 = vertical legend, 2 = box legend
`textSize`	font size
`boxColor`	color of box behind legend
`alpha`	alpha value of box behind legend

Value

gp of fluorescence legend

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
                                    package = "SpatialOmicsOverlay")))

# image <- downloadMouseBrainImage()

# muBrain <- addImageOmeTiff(overlay = muBrain, 
#                           ometiff = image, res = 8)
                             
gp <- plotSpatialOverlay(overlay = muBrain,   
                         hiRes = FALSE, scaleBar = FALSE)
                         
legend <- fluorLegend(muBrain, nrow = 2, textSize = 3, boxColor = "red")

cowplot::ggdraw() + 
    cowplot::draw_plot(gp) +
    cowplot::draw_plot(legend, scale = 0.12, x = -0.3, y = -0.25)

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
                                    package = "SpatialOmicsOverlay")))

# image <- downloadMouseBrainImage()

# muBrain <- addImageOmeTiff(overlay = muBrain, 
#                           ometiff = image, res = 8)
                             
gp <- plotSpatialOverlay(overlay = muBrain,   
                         hiRes = FALSE, scaleBar = FALSE)
                         
legend <- fluorLegend(muBrain, nrow = 2, textSize = 3, boxColor = "red")

cowplot::ggdraw() + 
    cowplot::draw_plot(gp) +
    cowplot::draw_plot(legend, scale = 0.12, x = -0.3, y = -0.25)

Move coordinates if they don't match image

Description

If generated coordinates do not match the image use this function to move coordinates. Coordinates are only changed 1 pixel at a time.

Usage

moveCoords(overlay, direction = "right")
moveCoords(overlay, direction = "right")

Arguments

`overlay`	SpatialOverlay object
`direction`	which direction should coordinates move: left, right, up, down

Value

SpatialOverlay object

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))
head(coords(muBrain), 3)
head(coords(moveCoords(muBrain, direction = "up")), 3)                                    

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))
head(coords(muBrain), 3)
head(coords(moveCoords(muBrain, direction = "up")), 3)

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, ...)
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)

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)

Parse the xml file for the scan metadata of GeoMx images

Description

Parse the xml file for the scan metadata of GeoMx images

Usage

parseScanMetadata(omexml)
parseScanMetadata(omexml)

Arguments

omexml

xml file from OME-TIFF, can provide path to OME-TIFF and xml will automatically be extracted

Value

metadata for entire scan

Examples


image <- downloadMouseBrainImage()

xml <- xmlExtraction(ometiff = image)

scan_metadata <- parseScanMetadata(omexml = xml)

image <- downloadMouseBrainImage()

xml <- xmlExtraction(ometiff = image)

scan_metadata <- parseScanMetadata(omexml = xml)

overlay plots

Description

overlay plots

Usage

plotSpatialOverlay(
  overlay,
  colorBy = "sampleID",
  hiRes = TRUE,
  alpha = 1,
  legend = TRUE,
  scaleBar = TRUE,
  image = TRUE,
  fluorLegend = FALSE,
  ...,
  corner = "bottomright",
  scaleBarWidth = 0.2,
  scaleBarMicrons = NULL,
  scaleBarColor = NULL,
  scaleBarFontSize = 6,
  scaleBarLineSize = 1.5,
  textDistance = 2
)
plotSpatialOverlay(
  overlay,
  colorBy = "sampleID",
  hiRes = TRUE,
  alpha = 1,
  legend = TRUE,
  scaleBar = TRUE,
  image = TRUE,
  fluorLegend = FALSE,
  ...,
  corner = "bottomright",
  scaleBarWidth = 0.2,
  scaleBarMicrons = NULL,
  scaleBarColor = NULL,
  scaleBarFontSize = 6,
  scaleBarLineSize = 1.5,
  textDistance = 2
)

Arguments

`overlay`	SpatialOverlay object
`colorBy`	annotation to color by
`hiRes`	generated figures are either high resolution or print quickly. Note: hiRes and outline ggplots use fill, lowRes uses color
`alpha`	opacity of overlays
`legend`	should legend be plotted
`scaleBar`	should scale bar be plotted
`image`	should image be plotted, image must be added to SpatialOverlay object
`fluorLegend`	should viz marker on the image be added to legend
`...`	additional parameters for scale bar line & text, will affect both
`corner`	where in the figure should the scale bar be printed. Options: "bottomright" "topright" "bottomleft" "topleft" "bottomcenter" "topcenter"
`scaleBarWidth`	percent of total figure the scale bar should take up
`scaleBarMicrons`	specific microns to set scale bar at, overrides scaleBarWidth if set
`scaleBarColor`	scale bar & text color
`scaleBarFontSize`	font size
`scaleBarLineSize`	width of line
`textDistance`	text's distance from scale bar.

Value

Note

hiRes and outline ggplots use fill, lowRes uses color

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
                                    package = "SpatialOmicsOverlay")))
                             
plotSpatialOverlay(overlay = muBrain, legend = FALSE,  
                   hiRes = FALSE, scaleBar = FALSE)

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
                                    package = "SpatialOmicsOverlay")))
                             
plotSpatialOverlay(overlay = muBrain, legend = FALSE,  
                   hiRes = FALSE, scaleBar = FALSE)

Read lab worksheet into dataframe of annotations

Description

Read lab worksheet into dataframe of annotations

Usage

readLabWorksheet(lw, slideName, roiCol = NULL, slideCol = NULL)
readLabWorksheet(lw, slideName, roiCol = NULL, slideCol = NULL)

Arguments

`lw`	lab worksheet file path
`slideName`	name of slide
`roiCol`	column containing ROI information, if NULL function will determine automatically
`slideCol`	column containing slide name, if NULL function will determine automatically

Value

df of ROI annotations

Examples


muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

Read in `SpatialOverlay` from tiff file and annotations

Description

Create an instance of class SpatialOverlay by reading data from OME-TIFF and annotation sheet.

Usage

readSpatialOverlay(
  ometiff,
  annots,
  slideName,
  image = FALSE,
  res = NULL,
  saveFile = FALSE,
  outline = TRUE,
  ...,
  segCol = NULL
)
readSpatialOverlay(
  ometiff,
  annots,
  slideName,
  image = FALSE,
  res = NULL,
  saveFile = FALSE,
  outline = TRUE,
  ...,
  segCol = NULL
)

Arguments

`ometiff`	path to OME-TIFF
`annots`	path to annotation file: can be labWorksheet, DA excel file, or delimted file
`slideName`	name of slide
`image`	should image be extracted from OME-TIFF
`res`	resolution of image 1 = largest, higher number = smaller This value will affect the coordinates of the overlays. res = 2, resolution is 1/2 the size as the raw image res = 3, resolution is 1/4 the size as the raw image res = 4, resolution is 1/8 the size as the raw image resolution = 1/2^(res-1)
`saveFile`	should xml & image be saved, file is saved in working directory with same name as OME-TIFF
`outline`	returned coordinates only contain outlinearies, will not work for segmented ROIs
`...`	additional parameters for 'readLabWorksheet' like 'roiCol' and 'slideCol'
`segCol`	additional parameter for ‘annotMatching' if default search doesn’t work. For default search, set to NULL

Value

SpatialOverlay of slide

Examples


muBrain_GxT <- readRDS(unzip(system.file("extdata", "muBrain_GxT.zip", 
                         package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- readSpatialOverlay(ometiff = image, annots = muBrain_GxT[,1:5], 
                              slideName = "D5761 (3)", image = TRUE, res = 8, 
                              saveFile = FALSE, outline = FALSE)

muBrain_GxT <- readRDS(unzip(system.file("extdata", "muBrain_GxT.zip", 
                         package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- readSpatialOverlay(ometiff = image, annots = muBrain_GxT[,1:5], 
                              slideName = "D5761 (3)", image = TRUE, res = 8, 
                              saveFile = FALSE, outline = FALSE)

recolor images after changing colors and/or color intensities

Description

recolor images after changing colors and/or color intensities

Usage

recolor(overlay)
recolor(overlay)

Arguments

overlay

SpatialOverlay object

Value

SpatialOverlay object with RGB image

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

muBrain <- changeImageColoring(overlay = muBrain, color = "magenta", 
                               dye = "Cy5")
showImage(recolor(muBrain))

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

image <- downloadMouseBrainImage()

muBrain <- add4ChannelImage(overlay = muBrain, 
                            ometiff = image, res = 8)

muBrain <- changeImageColoring(overlay = muBrain, color = "magenta", 
                               dye = "Cy5")
showImage(recolor(muBrain))

Remove sample(s) from SpatialOverlay

Description

Remove sample(s) from SpatialOverlay

Usage

removeSample(overlay, remove)
removeSample(overlay, remove)

Arguments

`overlay`	SpatialOverlay object
`remove`	sampNames of overlay to remove

Value

SpatialOverlay object without samples in remove

Examples


muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

samps <- muBrainLW$Sample_ID[muBrainLW$segment != "Full ROI"]

muBrainSub <- removeSample(overlay = muBrain, remove = samps)

muBrain
muBrainSub

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip", 
                                    package = "SpatialOmicsOverlay")))

muBrainLW <- system.file("extdata", "muBrain_LabWorksheet.txt", 
                         package = "SpatialOmicsOverlay")

muBrainLW <- readLabWorksheet(muBrainLW, slideName = "D5761 (3)")

samps <- muBrainLW$Sample_ID[muBrainLW$segment != "Full ROI"]

muBrainSub <- removeSample(overlay = muBrain, remove = samps)

muBrain
muBrainSub

Class to Contain NanoString Spatial Overlay Images and Data

Description

The SpatialOverlay class organizes the pertinant information from the OME-TIFFs allowing for plotting on top of or beside the image

Usage

  SpatialOverlay(slideName,
                 scanMetadata,
                 overlayData,
                 coords = NULL,
                 plottingFactors = NULL,
                 workflow = list(outline=FALSE,
                                 labWorksheet=TRUE,
                                 scaled=FALSE),
                 image = list(filePath = NULL,
                              imagePointer = NULL,
                              resolution = NULL))
SpatialOverlay(slideName,
                 scanMetadata,
                 overlayData,
                 coords = NULL,
                 plottingFactors = NULL,
                 workflow = list(outline=FALSE,
                                 labWorksheet=TRUE,
                                 scaled=FALSE),
                 image = list(filePath = NULL,
                              imagePointer = NULL,
                              resolution = NULL))

Arguments

`slideName`	The name of the slide in the `SpatialOverlay` object
`scanMetadata`	A `list` containing the scan metadata: panel(s) used, Physical sizes (x,y) for scale bar, fluorescence data, and segmentation info
`overlayData`	An `SpatialPosition` containing individiual sample info: SampleID, Height, Width, X&Y coordinates in overall scan, segmentation, and base64 encoded position
`coords`	An optional `data.frame` with coordinates derived from the encoded position.
`plottingFactors`	An optional `data.frame` with annotations to plot on. These can be added using `addPlottingFactor`
`workflow`	A `list` containing meta-data on the processing workflow including `"outline"`, `"labWorksheet"`, & `"scaled"`. These booleans are kept automatically in `readSpatialOverlay` and are used for logic gates in downstream processing
`image`	A `list` containing location of and pointer to the image: `"filePath"`, `"imagePointer"`, & `"resolution"`

Value

An S4 class containing image data from a NanoString GeoMx experiment

Accessing

SpatialOverlay objects have the following accessor methods:

sampNames(object): extracts the sample names of each ROI in the slide.
slideName(object): extracts the slide name.
overlay(object): extracts the SpatialPosition information for each ROI.
scanMeta(object): extracts the scan metadata.
scanMeta(object): coords(object): extracts the coordinates for the entire scan.
plotFactors(object): extracts avaliable plotting factors.
labWork(object): extracts the boolean if a lab worksheet was used.
outline(object): extracts the boolena if only the outline points were generated.
seg(object): extracts if there are any segmented ROIs in the slide.
scaleBarRatio(object): extracts the scale bar ratio from scanMeta for the X axis
fluor(object): extracts fluorenscence information for the scan.
showImage(object): prints image.
res(object): extracts resolution of image.
workflow(object): extracts workflow data.
scaled(object): extracts if coordinates have been scaled.
imageInfo(object): extracts image data.

Class to Contain NanoString Spatial Overlay ROI information

Description

The SpatialPosition class organizes the pertinant ROI specific information from the OME-TIFFs

Usage

  SpatialPosition(position)
SpatialPosition(position)

Arguments

position

data.frame containing information from the OME-TIFF:

"ROILabel" order of ROIs

"Sample_ID" unique identifier

"Height" total height of ROI

"Width" total width of ROI

"X" top left corner (x coordinate) of ROI in total scan

"Y" top left corner (y coordinate) of ROI in total scan

"Segmentation" part of segmented ROI

"Position" base64 encoding of coordinates

Value

An S4 class containing image data from a NanoString GeoMx experiment

Accessing

SpatialPosition objects have the following accessor methods:

spatialPos(object): returns SpatialPosition object
meta(object): extracts the metadata for each ROI, does not include the base64 encoding.
position(object): extracts the base64 encoding for each ROI, CAUTION: very long strings.

Extract xml from OME-TIFF

Description

Extract xml from OME-TIFF

Usage

xmlExtraction(ometiff, saveFile = FALSE, outdir = NULL)
xmlExtraction(ometiff, saveFile = FALSE, outdir = NULL)

Arguments

`ometiff`	path to OME-TIFF
`saveFile`	should xml be saved, file is saved in working directory with same name as OME-TIFF
`outdir`	output directory for saved xml. If NULL, saved in same directory as OME-TIFF

Value

list of xml data

Examples


image <- downloadMouseBrainImage()
xml <- xmlExtraction(ometiff = image)

image <- downloadMouseBrainImage()
xml <- xmlExtraction(ometiff = image)

Package 'SpatialOmicsOverlay'

Help Index

Add 4-channel image to SpatialOverlay from OME-TIFF. Allows for recoloring of image

Description

Usage

Arguments

Value

Examples

Add image to SpatialOverlay from disk

Description

Usage

Arguments

Value

Add image to SpatialOverlay from OME-TIFF

Description

Usage

Arguments

Value

Examples

Add plotting factor to SpatialOverlay object

Description

Usage

Arguments

Value

Examples

Match ROIs in annotation file to xml

Description

Usage

Arguments

Value

Print long string in more managable fashion

Description

Usage

Arguments

Value

Examples

Update color intensities for changing to RGB image

Description

Usage

Arguments

Value

Examples

Update color scheme for changing to RGB image

Description

Usage

Arguments

Value

Examples

Determine lowest resolution image in OME-TIFF

Description

Usage

Arguments

Value

Examples

Create coordinate file for entire scan

Description

Usage

Arguments

Value

Examples

Create a binary mask from a base 64 string

Description

Usage

Arguments

Value

Examples

Crop to zoom in on given ROIs

Description

Usage

Arguments

Value

Examples

Crop to remove black boundary around tissue.

Description

Usage

Arguments

Value

Examples

Download Mouse Brain OME-TIFF from NanoString's Spatial Organ Atlas

Description

Add plotting factor to `SpatialOverlay` object

Read in `SpatialOverlay` from tiff file and annotations