#### 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
2. 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
3. The function returns a um value in valid sizes.
test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L137
4. 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
2. 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
3. The function returns a um value in valid sizes.
test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L308
4. 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
2. The function returns a list of numeric values.
test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L153
3. 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
2. The function returns a list of numeric values.
test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L324
3. 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
2. The function produces a ggplot object.
test: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/blob/8d0039f4f5f676885cded726703212875d5abcd2/tests/testthat/test_plotting.R#L398
3. 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
