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

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specs.md

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

Specs for addImageOmeTiff:

  1. The function outputs a list in the image slot containing the expected filePath, imagePointer, and resolution. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L13
  2. The imagePointer is a magick-image with the correct dimensions. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L28
  3. The function scales the coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L44
  4. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L38
  5. The function must have SpatialOverlay object input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L9

Specs for add4ChannelImage:

  1. The function outputs a list in the image slot containing the expected filePath, imagePointer, and resolution. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L85
  2. The imagePointer is an AnnotatedImage with the correct dimensions. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L100
  3. The function scales the coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L109
  4. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L129
  5. The function must have SpatialOverlay object input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L81

Specs for addImageFile:

  1. The function outputs a list in the image slot containing the expected filePath, imagePointer, and resolution. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L146
  2. The imagePointer is a magick-image with the correct dimensions. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L156
  3. The function scales the coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L167
  4. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L162
  5. The function must have SpatialOverlay object input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L142

Specs for addPlottingFactor:

  1. The function only works on one factor at a time regardless of input type. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L14
  2. The function gives warning for annotation missing for samples in object regardless of input type. test:https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L29
  3. The function works with a data.frame input, column name plotting factor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L16
  4. The function works with a data.frame input, row name plotting factor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L31
  5. The function works with a matrix input, column name plotting factor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L51
  6. The function works with a matrix input, row name plotting factor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L65
  7. If vectors aren't named they must be the same length as number of samples in object. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L83
  8. The function only matches vectors if they are named, otherwise assumed in correct order. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L90
  9. The function works with character vectors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L92
  10. The function works with factor vectors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L117
  11. The function works with numeric vectors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L143
  12. The function works with a NanostringGeomxSet input, column name plotting factor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L173
  13. The function works with a NanostringGeomxSet input, row name plotting factor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L182
  14. The function can handle NULL inputs. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addPlottingFactor.R#L42

Specs for decodeB64:

  1. The function produces same values as python truth. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L19

Specs for createMask:

When outline == FALSE,

  1. The function creates mask in correct dimension. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L31
  2. The function produces same values as python truth. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L33
  3. The function produces mask of only 0 & 1. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L35
  4. The function creates matrix. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L37

When outline == TRUE,

  1. The function creates mask in correct dimension. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L59
  2. The function has fewer matches with the python truth. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L61
  3. The function produces mask of only 0 & 1. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L64
  4. The function creates matrix. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L66
  5. The function create mask with < 0.1% of points with 7 or more neighbors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L69

Specs for coordsFromMask:

When outline == FALSE,

  1. The function creates coordinates for mask = 1 points. Coordinates are put into full image range and changed from base1 to base0. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L42

When outline == TRUE,

  1. The function creates coordinates for mask = 1 points. Coordinates are put into full image range and changed from base1 to base0. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L74

Specs for pencilCoordSorting:

  1. The function sorts outline coordinates by proximity. >99% of differences between adjacent coordinates is 1. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L101
  2. The function sorts outline coordinates by proximity. The max difference is <100. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L104

Specs for createCoordFile:

  1. The function places coordinates in correct location. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L124
  2. The function produces same values as python truth. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L131
  3. The function only returns outline coordinates on Geometric data. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L143
  4. The function must have SpatialOverlay object input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L118

Specs for Boundary:

  1. The function returns expected number of neighbors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L153

Specs for moveCoords:

  1. The function moves only expected coordinate by 1. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_coordinateGeneration.R#L176

Specs for scaleCoords:

  1. The function scales the coordinates based on the size of the image. test:https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L48
  2. The coordinates are all smaller than the image size. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L56
  3. There are no duplicated coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L63
  4. Coordinates can't be rescaled. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L69
  5. An image must be in object to scale coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_addImage.R#L72

Specs for xmlExtraction:

  1. The function only works with valid ometiff file. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L4
  2. The function returns a valid list with the expected names. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L13
  3. The function saves xml file in expected location, if desired. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L20
  4. The function doesn't save file when not asked. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L29

Specs for imageExtraction:

  1. The function only extracts valid res layers. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L39
  2. The function extracts expected res layer. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L42
  3. The function saves file in expected location and in correct & valid fileType. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L52

Specs for checkValidRes:

  1. The function returns expected value. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_extraction.R#L88

Specs for cropTissue:

  1. The function returns smaller image. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L14
  2. The function returns all original coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L20
  3. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L23
  4. The function requires valid input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L7

Specs for cropSamples:

  1. The function requires valid input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L37

When sampsOnly = TRUE,

  1. The function returns smaller image. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L48
  2. The function returns all coordinates of only the given samples. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L54
  3. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L59

When sampsOnly = FALSE

  1. The function returns smaller image. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L64
  2. The function returns all coordinates of the given samples. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L70
  3. The function returns coordinates within dimensions of cropped image. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L75
  4. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L86
  5. The function only works with valid sampleIDs. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L89

Specs for flipX:

  1. The function returns expected coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L111
  2. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L116
  3. The function requires valid input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L106

Specs for flipY:

  1. The function returns expected coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L126
  2. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L131
  3. The function requires valid input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L121

Specs for changeColoringIntensity:

  1. The function only works on 4-channel images. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L136
  2. The function changes min/max intensity values of only correct fluor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L148

Specs for changeImageColoring:

  1. The function only works on 4-channel images. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L140
  2. The function changes ColorCode values of only correct fluor. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L170

Specs for imageColoring:

  1. The function creates RGB image arrays. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L195
  2. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L200

Specs for recolor:

  1. The function scales coordinates. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L212
  2. The function creates RGB image arrays. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L220
  3. The function produces reproducible results. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L226
  4. The function requires valid input. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_imageManipulation.R#L205

Specs for parseScanMetadata:

  1. The function works on ometiff variable instead of expected xml. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L12
  2. The function returns a list with all of the expected names. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L18

Specs for fluorData:

  1. The function works on xmls where fluor data takes up 1 or 2 lines. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L44
  2. The function returns a data.frame with all of the expected values. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L72

Specs for physicalSizes:

  1. The function works returns list with expected names & values. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L91

Specs for parseOverlayAttrs:

  1. The function requires correct inputs.. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L105
  2. The function only works with valid sample names. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L117
  3. The function returns SpatialPosition with correct column names. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L128

Specs for annotMatching:

  1. The function matches sampleIDs correctly between xml and annots. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_parsing.R#L144

Specs for plotSpatialOverlay:

  1. The function requires valid colorBy variable. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L22
  2. The function returns a ggplot object for high resolution, low resolution and outline graphing. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L31
  3. The function returns a ggplot object without legend if desired. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L52
  4. The function returns a ggplot object with fluorescence legend if desired. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L59
  5. The function works on with both 4-channel and RGB images. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L252
  6. The function produces reproducible figures. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L38

Specs for scaleBarMath:

Using scaleBarWidth 1. The function expects size to be between 0-1. test:https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L114

Without image

  1. The function returns a list with the expected names and values. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L119
  2. The function returns a um value in valid sizes. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L137
  3. The function calculates the number of pixels for scale bar correctly. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L143

With image

  1. The function returns a list with the expected names and values. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L290
  2. The function returns a um value in valid sizes. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L308
  3. The function calculates the number of pixels for scale bar correctly. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L314

Using scaleBarMicrons 1. The function uses scaleBarWidth if scaleBarMicrons is not set. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/fc532b5aaa10d3f0aed6354c38b18a8b86cf2434/tests/testthat/test_plotting.R#L129 2. The function sets scale bar to be equal to scaleBarMicrons. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/fc532b5aaa10d3f0aed6354c38b18a8b86cf2434/tests/testthat/test_plotting.R#L131 3. The function uses scaleBarWidth if scaleBarMicrons is not valid. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/fc532b5aaa10d3f0aed6354c38b18a8b86cf2434/tests/testthat/test_plotting.R#L133

Specs for scaleBarCalculation:

  1. The function only works with valid corner value. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L149

Without image

  1. The function returns a list of numeric values. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L153
  2. The function calculates the scale bar points the same across the different corner options. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L157

With image

  1. The function returns a list of numeric values. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L324
  2. The function calculates the scale bar points the same across the different corner options. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L328

Specs for scaleBarPrinting:

Without image,

  1. The function only works with valid corner value. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L227
  2. The function produces a ggplot object. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L232
  3. The function produces reproducible figures. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L236

With image

  1. The function produces a ggplot object. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L398
  2. The function produces reproducible figures. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L402

Specs for fluorLegend:

  1. The function only works on valid nrow values. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L408
  2. The function produces reproducible legends. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L412

Specs for readSpatialOverlay:

  1. The function works with either a labworksheet or a geomxset object as annotation. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L13
  2. The function only returns samples in both xml and annotation. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L25

With all points

  1. The function returns a SpatialOverlay object. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L32
  2. The function returns a SpatialOverlay object with the expected values in the correct locations. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L35

With image

  1. The function returns a SpatialOverlay object. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L62
  2. The function returns a SpatialOverlay object with the expected values in the correct locations. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L65
  3. The function returns a SpatialOverlay object with image in expected location. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L82
  4. The function returns a SpatialOverlay object with scaled coordinates to image. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L88

With boundary points

  1. The function returns a SpatialOverlay object. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L97
  2. The function returns a SpatialOverlay object with the expected values in the correct locations. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_readSpatialOverlay.R#L100

Specs for removeSamples:

  1. The function only works on valid sample names. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_removeSamples.R#L25
  2. The function works before adding coordinates and plotting factors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_removeSamples.R#L32
  3. The function works after adding coordinates and before plotting factors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_removeSamples.R#L50
  4. The function works after adding coordinates and plotting factors. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_removeSamples.R#L68

Specs for SpatialOverlay-class:

  1. The class is formatted correctly. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_SpatialOverlay.R#L15
  2. The class accessors work as expected. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_SpatialOverlay.R#L43

Specs for SpatialPosition-class:

  1. The class is formatted correctly. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_SpatialPosition.R#L9
  2. The class accessors work as expected. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_SpatialPosition.R#L30

Specs for bookendStr:

  1. The function returns a string in the expected format. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_utils.R#L3

Specs for readLabWorksheet:

  1. The function only works on correct file paths. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_utils.R#L24
  2. The function only works on correct slide names. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_utils.R#L27
  3. The function only returns annotations from the specified slide. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_utils.R#L31

Specs for downloadMouseBrainImage:

  1. The function downloads the mouse brain tiff and returns a valid file path. test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_utils.R#L51


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

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