v0.3.5

GiottoClass 0.3.5 (2024/08/28)

breaking changes

• set_giotto_python_path() will now also initialize python env to set by default and print which python env is active, but otherwise do nothing if any python env has already been initialized.
• deprecated readGiottoInstructions(), showGiottoInstructions(), changeGiottoInstructions(), replaceGiottoInstructions() in favor of instructions() generic

bug fixes

• intensity images now automatically scale to estimated highest value
• giottoPolygon plot() default max_poly raised to 1e6
• giottoInstructions no longer lose class when specific params are replaced
• ometif_to_tif() now checks for imagecodecs package as well
• anndataToGiotto() and giottoToAnndata now check for anndata package as well.
• fix joinGiottoObjects() "z_stack" join method
• fix error in documentation #214 by shaojunyu
• fix error in installGiottoEnvironment() #1006 by 13954380607

enhancements

• print() method for giottoInstructions
• rbind() for spatLocsObj

v0.3.3

bug fixes

• fix flipping issue with giottoAffineImage for certain affine transforms

enhancements

• missing method for affine() instantiates an affine2d object

v0.1.0

Released with Giotto v4.0.0

Giotto Class 0.1.0 (23/11/28)

Breaking Changes

• Giotto subsetting rework

Added

• Added terraVectData as virtual parent class for giottoPolygon and giottoPoints classes
• Added $ and $<- methods for terraVectData
• Added ext<-() method for giottoPolygon, giottoPoints
• Added crop() method for giottoLargeImage, giottoPoints
• Added [ subsetting for giottoPoints and giottoPolygon with numerical, logical, and character (by ID)
• Added as.sf() and as.stars() converters for giottoPoints and giottoPolygon
• Added setGiotto() generic
• Added gap param to tessellate() which introduces a variable gap between the polygons tessellated
• Added triGrid()
• Added orthoGrid()
• Added DelayedMatrixStats to suggests

Changes

• Improved performance of gefToGiotto()
• Updated spatIDs() and featIDs() methods for giottoPolygon and giottoPoints to allow returning non-unique IDs
• Added check for plot() when giottoPolygon or giottoPoints objects contain no geometries
• Added warning for crop() when giottoLargeImage, giottoPolygon, giottoPoints objects are being cropped with an extent that does not include any information
• Changed: Conversion of createGiottoPoints() to a generic function
• Deprecate: radius param in favor of shape_size for tessellate()
• Fixed: python install_github_link_pip() param
• Fixed: python create_Anndata added to globals.R