reqs.md

In Nanostring-Biostats/SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data

Reqs for addImageOmeTiff:

• The user input overlay, a SpatialOverlay object
• The user input ometiff file path (default NULL)
• The user input the res(olution) image layer to extract from the OMETIFF (default NULL)
• The user can input extra variables for imageExtraction function
• The function outputs a SpatialOverlay object
  • The function outputs extracted RGB image in object
  • The function outputs calculates and scales coordinates if initial image or at a different resolution

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-addimageometiff

Reqs for addImageFile:

• The user input overlay, a SpatialOverlay object
• The user input imageFile path for non-OMETIFF image (default NULL)
• The user input the res(olution) image layer extracted from the OMETIFF (default NULL)
• The function outputs a SpatialOverlay object
  • The function outputs image in object
  • The function outputs calculates and scales coordinates if initial image or at a different resolution

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-addimagefile

Reqs for add4ChannelImage:

• The user input overlay, a SpatialOverlay object
• The user input ometiff file path (default NULL)
• The user input the res(olution) image layer to extract from the OMETIFF (default NULL)
• The user can input extra variables for imageExtraction function
• The function outputs a SpatialOverlay object
  • The function outputs extracted 4-channel image in object
  • The function outputs calculates and scales coordinates if initial image or at a different resolution

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-add4channelimage

Reqs for addPlottingFactor:

• The user input overlay, a SpatialOverlay object
• The user input annots, a NanoStringGeoMxSet, matrix, data.frame, or vector
• The user input the plottingFactor: column or row name from annots
• If using NanoStringGeoMxSet, the user input countMatrix in object to pull counts from (default "exprs")
• The function outputs a SpatialOverlay object
  • The function outputs plottingFactor in plotFactors
  • The function matches on SampleID or if unnamed vector assumes correct order

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-addplottingfactor

Reqs for createCoordFile:

• The user input overlay, a SpatialOverlay object
• The user input outline, only outline or all coordinates boolean (default = TRUE)
• The function outputs a SpatialOverlay object
  • The function outputs coordinates in coords
  • The function specifies workflow@scaled and workflow@outline
  • The function only returns outline coords on Geometric datasets
  • The function wraps all coordinate generating functions together to add to SpatialOverlay object

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-createcoordfile

Reqs for createMask:

• The user input b64string, a base64 encoded string containing AOI position
• The user input metadata, metadata of AOI including height and width
• The user input outline, only outline or all coordinates boolean (default = TRUE)
• The function outputs a binary mask matrix
  • The function outputs binary matrix containing AOI position
  • The function outputs matrix in metadata specified height and width
  • The function outputs only outline coordinates if specified, else all coordinates are output

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-createmask

Reqs for coordsFromMask:

• The user input mask, binary mask matrix
• The user input metadata, metadata of AOI including X,Y in full image
• The user input outline, only outline or all coordinates boolean (default = TRUE)
• The function outputs a data.frame of coordinate values
  • The function outputs data.frame containing X,Y coordinates of all AOIs in slide
  • The function changes coordinates from 1 base to 0 base
  • The function sorts coordinates if returning outline coords

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-coordsfrommask

Reqs for pencilCoordSorting:

• The user input coords for an AOI
• The user input rangeWidth, distance to look for closest coord (default = 100)
• The function outputs an ordered data.frame of coordinate values
  • The function outputs data.frame containing X,Y coordinates of all AOIs in slide ordered by proximity to the previous coordinate
  • The function does not repeat coordinates

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-pencilsortingcoords

Reqs for boundary:

• The user input mat, binary mask matrix
• The function outputs an vector
  • The function outputs vector of number of neighbors each point has

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-boundary

Reqs for moveCoords:

• The user input overlay, SpatialOverlay object
• The user input direction, direction to move coordinates
• The function outputs a SpatialOverlay object

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-moveCoords

Reqs for scaleCoords:

• The user input overlay, a SpatialOverlay object
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with coordinates scaled to image size
  • The function does not scale coordinates again if already scaled
  • The function does not scale coordinates if no image in object
  • The function only returns unique coordinates

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-scalecoords

Reqs for imageColoring:

• The user input omeImage, a 4-channel AnnotatedImage object
• The user input scanMeta, scan metadata including fluorescence info
• The function outputs a AnnotatedImage object
  • The function outputs an RGB AnnotatedImage object
  • The function scales to min and max intensity if given in scanMeta
  • The function adds 4-channel RGB together for final RGB matrix
  • The function normalizes RGB matrix

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-imagecoloring

Reqs for changeImageColoring:

• The user input overlay, a SpatialOverlay object with 4-channel image
• The user input color, new color hex or R color name
• The user input dye, Dye or DisplayName to change color of
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with fluorescence ColorCode updated
  • The function only works on objects with 4-channel images
  • The function only changes valid dye colors

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-changeimagecoloring

Reqs for changeColoringIntensity:

• The user input overlay, a SpatialOverlay object with 4-channel image
• The user input minInten, new minimum intensity value (default = NULL)
• The user input maxInten, new maximum intensity value (default = NULL)
• The user input dye, Dye or DisplayName to change color of
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with fluorescence MinIntensity and/or MaxIntensity updated
  • The function only works on objects with 4-channel images
  • The function only changes valid dye colors

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-changecoloringintensity

Reqs for recolor:

• The user input overlay, a SpatialOverlay object with 4-channel image
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with RGB image
  • The function only works on objects with 4-channel images
  • The function only scales coordinates if needed
  • The function crops to tissue

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-recolor

Reqs for flipY:

• The user input overlay, a SpatialOverlay object
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with Y axis flipped
  • The function flips image and coordinates

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-flipy

Reqs for flipX:

• The user input overlay, a SpatialOverlay object
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with X axis flipped
  • The function flips image and coordinates

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-flipx

Reqs for cropSamples:

• The user input overlay, a SpatialOverlay object
• The user input sampleIDs, sampleIDs of AOIs to include
• The user input buffer, percent of image to add on each edge (default = 0.1)
• The user input sampsOnly, only show given samples (default = TRUE)
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with cropped image and coordinates only showing given samples
  • The function only works on valid sampleIDs
  • The function only works on RGB images
  • The function requires coordinates to be generated
  • The function requires image in overlay
  • The function generates min/max coords to crop on given sampleIDs
  • The function filters coordinates to only given sampleIDs if desired

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-cropsamples

Reqs for cropTissue:

• The user input overlay, a SpatialOverlay object
• The user input buffer, percent of image to add on each edge (default = 0.05)
• The function outputs a SpatialOverlay object
  • The function outputs SpatialOverlay object with cropped image and coordinates minimizing black background around tissue
  • The function can work on 4-channel or RGB image
  • The function requires coordinates to be generated with RGB image
  • The function requires image in overlay
  • The function generates min/max coords to crop on tissue

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-croptissue

Reqs for xmlExtraction:

• The user input ometiff, file path
• The user input saveFile, boolean (default = FALSE)
• The function outputs a list
  • The function outputs list containing all xml info
  • The function only works on valid paths
  • The function saves file to same folder as ometiff if desired

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-xmlextraction

Reqs for imageExtraction:

• The user input ometiff, file path
• The user input res(olution), image layer to extract from the OMETIFF (default = 6)
• The user input scanMeta, scan metadata from XML (default = NULL)
• The user input saveFile, boolean (default = FALSE)
• The user input fileType, image type to save as (default = "tiff")
• The user input color, turn into RGB image boolean (default = TRUE)
• The function outputs an image
  • If color == TRUE
    • The function outputs magick-image pointer
    • The function colors image
    • The function saves image to same folder as ometiff if desired
    • The function only saves to valid fileTypes
  • If color == FALSE
    • The function outputs AnnotatedImage
  • The function only works on valid paths
  • The function only extracts valid res layers
  • The function extracts scanMeta if NULL

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-imageextraction

Reqs for checkValidRes:

• The user input ometiff, file path
• The function outputs an numeric
  • The function returns highest valid res(olution) value for ometiff

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-checkvalidres

Reqs for plotSpatialOverlay:

• The user input overlay, file path
• The user input colorBy, coloring factor (default = "sampleID")
• The user input hiRes(olution) plotting boolean (default = TRUE)
• The user input alpha, opacity value (default = 1)
• The user input legend, show legend boolean (default = TRUE)
• The user input scaleBar, show scale bar boolean (default = TRUE)
• The user input image, show image boolean (default = TRUE)
• The user input fluorLegend, show fluorescence legend (default = FALSE)
• The user input ..., extra values for scale bar plotting
• The user input corner, scale bar corner (default = "bottomright")
• The user input scaleBarWidth, scale bar width of image percentage (default = 0.2)
• The user input scaleBarMicrons, scale bar width in microns (default = NULL)
• The user input scaleBarColor, scale bar color (default = "black")
• The user input scaleBarFontSize, scale bar font size value (default = 6)
• The user input scaleBarLineSize, scale bar line size value (default = 1.5)
• The user input textDistance, distance of text from line value (default = 2)
• The function outputs a ggplot object
  • The function recolors image if 4-channel is given
  • The function only works on valid plotFactors unless sampleID is given
  • The function only adds fluorLegend if image = TRUE and desired regardless of plotting call
  • The function adds image to background if image = TRUE
  • The function uses image coordinates if image is attached even with image = FALSE
  • The function removes legend if desired
  • The function adds scalebar if desired
  • The function customizes scale bar

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-plotspatialoverlay

Reqs for scaleBarMath:

• The user input scanMetadata, scan metadata from XML specifically PhysicalX/Y
• The user input pts, coordinate data.frame
• The user input scaleBarWidth, percent of image value (default = 0.2)
• The user input scaleBarMicrons, scale bar width in microns (default = NULL)
• The user input image, image from SpatialOverlay (default = NULL)
• The function outputs a list
  • The function returns list of values to print scale bar
  • The function works with or without image
  • The function calculates scale bar width based on um/pixel ratio
  • The function works on all resolutions
  • The function only creates scale bars with round values

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/main/specs.md#specs-for-scalebarmath

Reqs for scaleBarCalculation:

• The user input corner, location for scale bar (default = "bottomright")
• The user input scaleBar, list from scaleBarMath
• The user input textDistance, distance of text from line value (default = 2)
• The function outputs a data.frame
  • The function returns data.frame of coordinates for scale bar
  • The function only works with valid corner
  • The function calculates scale bar coordinates

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-scalebarcalculation

Reqs for scaleBarPrinting:

• The user input gp, ggplot object
• The user input scaleBar, list from scaleBarMath
• The user input corner, distance of text from line value (default = 2)
• The user input scaleBarFontSize, scale bar font size value (default = 6)
• The user input scaleBarLineSize, scale bar line size value (default = 1.5)
• The user input scaleBarColor, scale bar color (default = "red)
• The user input textDistance, distance of text from line value (default = 2)
• The user input image, image from SpatialOverlay (default = NULL)
• The user input ..., extra values for scale bar plotting
• The function outputs a ggplot object
  • The function returns ggplot with added scale bar
  • The function works with or without image
  • The function customizes scale bar

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-scalebarprinting

Reqs for fluorLegend:

• The user input overlay, SpatialOverlay object
• The user input nrow, number of rows value (default = 4)
• The user input textSize, font size value (default = 10)
• The user input boxColor, color of background (default = "grey")
• The user input alpha, opacity value (default = 0.25)
• The function outputs a ggplot object
  • The function returns ggplot of visualization marker legend
  • The function only works with valid nrows
  • The function colors Target based on ColorCode
  • The function adds background based on user input

Specifications:

Reqs for readSpatialOverlay:

• The user input ometiff, file path
• The user input annots, file path or GeomxSet object
• The user input slideName, name of slide
• The user input image, add image boolean (default = FALSE)
• The user input res, image layer to extract from the OMETIFF (default = NULL)
• The user input saveFile, save file boolean (default = FALSE)
• The user input outline, outline coords only boolean (default = TRUE)
• The function outputs a SpatialOverlay object
  • The function returns starting point SpatialOverlay
  • The function annotations can be NanostringGeomxSet, labWorksheet, or DSPDA output
  • The function is a wrapper for extracting XML, add scan metadata, add overlay attrs, determine dataset segmentation, add image, generate coordinates

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-readspatialoverlay

Reqs for removeSample:

• The user input overlay, SpatialOverlay object
• The user input remove, sampleIDs to remove
• The function outputs a SpatialOverlay object
  • The function returns a SpatialOverlay without sampleIDs to remove
  • The function only works on valid sampleIDs
  • The function removes samples across all parts of the SpatialOverlay object
  • The function determines if dataset segmentation type

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-removesamples

Reqs for bookendStr:

• The user input x, string
• The user input bookend, length of bookend value (default = 8)
• The function outputs a string
  • The function returns a string small enough to be legible
  • The function returns first bookend ... last bookend (# total char)

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-bookendstr

Reqs for readLabWorksheet:

• The user input lw, labworksheet file path
• The user input slideName, slide name
• The function outputs a data.frame
  • The function returns a data.frame with AOI annotations
  • The function only works on valid lw
  • The function only works with valid slide name

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-readlabworksheet

Reqs for downloadMouseBrainImage:

• The function outputs a tiff file path
  • The function returns a cached tiff file path for Spatial Organ Atlas Mouse Brain OMETIFF
  • The function downloads and untars file if not already cached

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-downloadmousebrainimage

Reqs for parseScanMetadata:

• The user input omexml, xml list
• The function outputs a list
  • The function returns a list of scan metadata including panel, physical size and fluorescence data
  • The function can handle omexml being the file path to ometiff

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-downloadmousebrainimage

Reqs for parseOverlayAttrs:

• The user input omexml, xml list
• The user input annots, data.frame of annotations
• The user input labworksheet, is annot labworksheet boolean
• The function outputs a SpatialPosition
  • The function returns a list of AOI metadata including AOI height, width, and location
  • The function can handle xml files from multiple software versions
  • The function only returns AOIs in both XML and annots

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-parseoverlayattrs

Reqs for physicalSizes:

• The user input omexml, xml list
• The function outputs a list
  • The function returns a list of PhysicalSizes from xml

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-physicalsizes

Reqs for fluorData:

• The user input omexml, xml list
• The function outputs a data.frame
  • The function returns a data.frame of fluorescence data from xml including: dye, displayname, color, wavelength, target, exposuretime, colorcode, and min/max intensities if avaliable.
  • The function can work if fluorescence data takes 1 or 2 slots in XML

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-fluordata

Reqs for decodeB64:

• The user input b64string, base 64 location string
• The user input width, width of AOI
• The user input height, height of AOI
• The function outputs a vector
  • The function returns a binary vector of AOI position

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-decodeb64

Reqs for annotMatching:

• The user input annots, data.frame of annotations
• The user input ROInum, ROI number from xml
• The user input maskNum, number of masks in ROI
• The user input maskText, segment name
• The function outputs a data.frame
  • The function returns a data.frame of the matching sampleID
  • The function only works on valid ROInums
  • The function can work on multiple versions of the software

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-annotmatching

Reqs for SpatialOverlay-class:

• The class contains all info pertaining to image
  • The class contains slideName
  • The class contains scanMetadata
    • List of panel, physicalsize, and fluorescence
  • The class contains overlayData
    • SpatialPosition
  • The class contains coords
  • The class contains plottingFactors
    • Added individually
  • The class contains workflow
    • Workflow booleans that affect downstream analysis: outline, labworksheet, scaled
  • The class contains image
    • list of image related info: filePath, imagePointer, resolution
• The class contains accessors and replacers where neccesary

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-spatialoverlay-class

Reqs for SpatialPosition-class:

• The class contains all info pertaining to position in space
  • The class contains ROILabel
  • The class contains Sample_ID
  • The class contains Height
  • The class contains Width
  • The class contains X
  • The class contains Y
  • The class contains Segmentation
  • The class contains Position
    • Base64 encoded string
• The class contains accessors and replacers where neccesary

Specifications: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/specs.md#specs-for-spatialposition-class

Nanostring-Biostats/SpatialOmicsOverlay documentation built on Dec. 18, 2024, 9:26 a.m.