V0.3.2

[jiajic]

breaking changes

• python environment installation and how it relates to default settings such as .condarc may have changed.
• giottoImage name slot now requires character and will not accept NULL

bug fixes

• loadGiotto() no longer errors with similarly named spat_units or feat_types (e.g. "cell" and "new_cell" would previously throw an error)
• fix in giottoToSpatialExperiment()
• fix for giottoToSeuratV5 for cosmx mini dataset #989 by guillermoturiel
• fix issue with prints in createGiottoCosMxObject() #960 by GBeattie

enhancements

• verbose param for createNearestNetwork()
• checkGiottoEnvironment() in addition to full filepaths, also now supports name of environment or installation directory
• installGiottoEnvironment(), removeGiottoEnvironment() now have conda param for setting path to conda executable and envname param for specifying environment by name
• installGiottoEnvironment() now has confirm param for skipping path input checks
• t() for giotto now affects images as well.

new

• affine() for giottoPolygon, giottoPoints, spatLocsObj, giotto
• shear() for giottoPoints, giottoPolygon, spatLocsObj, affine2d
• affine2d class for accumulating linear transforms to be used with affine()
• initialize(), [, $, show(), plot(), methods for affine2d
• spin(), rescale, spatShift(), affine(), flip(), shear() t() methods for affine2d
• giottoAffineImage class for just-in-time affine transformed images
• initialize(), method for giottoLargeImage
• initialize(), ext(), crop(), rescale(), spatShift(), plot(), methods for giottoAffineImage
• rescale() method for giottoImage
• spin(), shear(), affine(), flip(), t() methods for giottoAffineImage and giottoLargeImage (which converts to giottoAffineImage)
• as() conversion from giottoLargeImage to giottoAffineImage
• .get_centroid_xy() internal for getting numeric centroid xy values of any object that responds to ext()
• .bound_poly() internal for generating a dummy polygon from the extent of any object that responds to ext()
• .aff_shift_2d(), .aff_shift_2d<-(), .aff_linear_2d, .aff_linear_2d()<- internals for accessing and manipulating affine matrices