NEWS.md

GiottoClass 0.4.2 (2024/10/30)

bug fixes

• fix default method setting in createNetwork() for "delaunay" networks
• fix y spacing of makePseudoVisium()

changes

• makePseudoVisium() micron_scale (multiplicative scalefactor to get micron scaled values) supercedes micron_size which used the inverse.

GiottoClass 0.4.1 (2024/10/28)

new

• buffer() for giottoPolygon, giottoPoints, spatLocsObj. Default is to crop by voronoi borders with settleGeom()
• settleGeom() for giottoPolygon and SpatVector for finding non overlapping borders determined by voronoi

GiottoClass 0.4.0 (2024/10/27)

breaking changes

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

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

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

GiottoClass 0.3.4 (2024/08/04)

bug fixes

• hotfix anndata matrix support #216 by wwang-chcn

GiottoClass 0.3.3 (2024/07/29)

bug fixes

• fix flipping issue with giottoAffineImage for certain affine transforms

enhancements

• missing method for affine() instantiates an affine2d object

GiottoClass 0.3.2 (2024/07/26)

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

GiottoClass 0.3.1 (2024/05/21)

bug fixes

• allow passing of additional params with setGiotto() with ...
• spatShift() can now perform z shifts when start spatLocsObj has no z information
• fix bug in joinGiottoObjects() after v0.3.0 where it looks for the now non-existent @largeImages slot
• fix bug in .update_image_slot() after v0.3.0 where a NULL @largeImages slot will result in an error
• fix bugs in spatShift() and rescale() methods for giotto when setting a default spat_unit and feat_type

enhancements

• joinGiottoObjects() extent detection and xshift defaults now depend on ext() of the gobject instead of any images (when available)
• joinGiottoObjects() now has a dry_run param for previewing where datasets will be spatially located after the join

new

• as() conversion from giottoLargeImage to array
• as.matrix() method for spatLocsObj()

GiottoClass 0.3.0 (2024/05/13)

breaking changes

• deprecation of reconnect_image_object(), reconnect_giottoImage_MG() and reconnect_giottoLargeImage() internals in favor of simpler reconnect() generic
• giotto @largeImage slot is removed. All images now exist in @images slot.
• backwards compatibility for S3 spatialNetworkObj removed
• Not finding a specific spatialNetworkObj with getSpatialNetwork() is now upgraded to an error instead of returning NULL to be in line with other accessors.
• backwards compatibility for bare data.table spatial coordinates information is removed

bug fixes

• fix plot() params passing for giottoPolygon when type = "centroid"
• fix ext() output for giottoImage
• spatShift() and rescale() now also affect gobject attached images #945 by rbutleriii

enhancements

• use faster terra::rasterize() and terra::plot() instead of scattermore::scattermoreplot() for giottoPoints plot() method
• plot() giottoPoints method now plots density when dens = TRUE
• show_max param in density() and hist() to plot the image object's max_window setting
• .identify_background_range_polygons() now finds any polygons larger than a threshold percentage than the overall extent of the SpatVector input.
• ext() can now be used with giotto objects #945 by rbutleriii
• ext()<- can now be used with giottoImage
• as conversion from giottoLargeImage to giottoImage (giottoImage is sampled)
• crop() works for spatialNetworkObj

new

• new spatValues() to get specific values from a giotto object in data.table format
• new ometif_to_tif to convert between .ome.tif and .tif
• new terra::density() and terra::hist() wrappers for giottoLargeImage

GiottoClass 0.2.3 (2024/03/12)

bug fixes

• fix saveGiotto with overwrite = TRUE #870 by rbutlerii
• fix plot() method param passing for giottoLargeImage. Ensure access to terra params

enhancements

• createGiottoPoints data.frame method can now select which columns to use with x_colname, y_colname, feat_ID_colname params
• giotto now responds to spatial manipulation generics: t(), flip(), rescale(), spatShift(), spin()
• spatUnit() and featType() are now vectorized
• internal get_spatial_locations_list() and get_spatial_network_list() accessors now accept ":all:" token to get all available, ignoring spat_unit

GiottoClass 0.2.2 (2024/03/01)

bug fixes

• fix createGiottoPolygonsFromMask() IDs being applied out of sync to mask values
• fix createGiottoPolygon() character method dispatch for raster inputs
• remove unused fix_multipart param in createGiottoPolygonsFromMask()
• fix giottoPolygon ID caching after rbind()

enhancements

• createGiottoPolygonsFromMask() now has ID_fmt param for finer control of automatic poly_ID generation
• .flip_spatvect() internal for flipping SpatVector across arbitrary x and y vals

GiottoClass 0.2.1 (2024/02/28)

breaking changes

• giotto slot versions supercedes OS_platform. Used for tracking GiottoClass version.

bug fixes

• fix subsetGiotto unused on argument
• fix giotto object saving when image intensities overlaps data are present.
• fix exprObj show() for small matrices
• fix giotto calculateOverlap() method when working with image intensities data.

new

• createNetwork() hub function for creation of Giotto NN and spatial networks directly from matrices. Mainly for developers and advanced users.
• edge_distances() for calculating euclidean distances from numeric m x n matrix (nodes) and a data.table with from and to cols that define node connections.

enhancements

• addCellMetadata() and addFeatMetadata() now support merging on the names of provided vector and factor data with metadata cell_ID/feat_ID.

GiottoClass 0.1.3 (2024/01/12)

bug fixes

• fix unexpected sorting in addCellMetadata() and addFeatMetadata() #853 by rbutleriii

new

• init_gobject param in loadGiotto() to control whether object initialization is also performed after load
• vignette for image tools

enhancements

• ID sorts now use gtools::mixedsort() #853 by rbutleriii
• more subobjects respond to colnames, rownames, dimnames
• plot() and show() now handle 3D spatLocsObj

GiottoClass 0.1.2 (2024/01/02)

Added

• Added: max_window and colors slots to giottoLargeImage. Use GiottoClass:::.update_giotto_image() to update outdated objects.
• Added: .bitdepth() internal function to detect image bitdepth from sampled values
• Added: re-export getMonochromeColors() from GiottoUtils
• Added: giottoPolygon, giottoLargeImage method for calculateOverlap()
• Added: vignette for working with spatial classes
• Added: output param to .spatraster_sample_values(). Can now return as sampled data.frame, array, magick, EBImage

bug fixes

• param fixes in raster calculateOverlap() workflows

GiottoClass 0.1.1 (2023/12/16)

Breaking Changes

• Removed: getRainbowColors() to GiottoUtils
• Removed: get_prev_fname() and get_args() to GiottoUtils
• Removed: aggregateStacksPolygonsOLD()

Added

• Added: .gstop() for GiottoClass specific errors
• Added: plot() method for dimObj
• Added: ncol() and nrow() methods for dimObj
• Added: dimObj additional info now accessible using $ and $<-
• Added: spatEnrObj cols now accessible using $ and $<-
• Added: evaluate_input() as exported wrapper for evaluate functions
• Added: as.polygons() data.frame method for correctly formatted data.tables (replaces internal dt_to_spatvector_polygon())
• Added: as.polygons() data.frame method for correctly formatted data.tables (replaces internal dt_to_spatvector_points())
• Added: autocompletes for $ with spatLocsObj, spatEnrObj, dimObj, cellMetaObj, featMetaObj, giottoPolygon, giottoPoints
• Added: toplevel_params param to subsetGiottoLocs()
• Added: spin, spatShift, rescale methods for data.frame

Changes

• Fixed: Provenance now not accidentally created as a list in addSpatialCentroidLocations()
• Changed: giottoPolygon plot() now automatically switches to centroid plotting with more than 1e4 polys
• Changed: Package internal functions now have . prefix

GiottoClass 0.1.0 (2023/11/29)

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
• Added: calculateOverlap() and overlapToMatrix() as generic functions for feature and image overlap aggregations

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