GiottoClass v0.4.0

[jiajic]

breaking changes

• stop exporting deprecated internal accessors
• terra requirement raised to 1.7.41 for minCircle()
• R version raised to 4.4.1

bug fixes

• fix dimnames() for some subobjects
• fix joinGiottoObject() for gobjects with only poly and point data #233
• fix joinGiottoObject() for gobjects with image intensity overlaps features
• fix subsetting error due to expression matrix drop to numeric when only one cell is left
• shift_vertical_step and shift_horizontal_step args in createGiottoPolygonsFromMask() when numeric now shift by steps based on the dims of the image instead of just by the numerical value provided.
• fix feature metadata not being mixedsorted after join
• fix non-inclusive subsetting when not all minmax values are supplied to subsetGiottoLocs()
• fix giottoAffineImage loading after being saved

enhancements

• python packages to install through pip is now settable in installGiottoEnvironment() #224
• giotto initialize() and slot checking behavior can be toggled now using 'giotto.init' and 'giotto.check_valid' options. #946 by rbutleriii
• setGiotto() now only initializes and performs checks once all items are added if a list input is provided.
• instructions() with no args will now call createGiottoInstructions(). You can also supply named args.
• instructions(gobject, param) and instructions(gobject, param)<- will now work for giottoInstructions objects for convenience.
• [, [[, $, $<-, and subset() for giotto see ?GiottoClass::subset_giotto
• subset for spatIDs() and featIDs()
• objName(), spatUnit(), featType() generics now return NA_character_ instead of erroring when used on unsupported classes.
• ext() and ext<-() can now be used to get and set extent of affine2d
• rownames(), colnames(), dimnames() for giotto
• spatValues() can get values from multiple spatial units.
• createGiottoPolygonsFromMask() now works with anything terra::rast() can read
• createGiottoLargeImage() now works with anything terra::rast() can read

new

• sliceGiotto() for pulling out specific spatial units and feature types as independent giotto objects
• splitGiotto() for splitting a Giotto object into a list of Giotto objects based on a cell metadata column
• as.list() method for giotto to dump the data as a list of subobjects
• XY() and XY<-() for accessing and setting coordinate values of subobjects as matrix
• terra convHull(), minRect(), minCircle() for Giotto spatial vector classes
• area() for SpatVector and giottoPolygon