Changelog • GiottoClass

GiottoClass 0.2.3 (2024/03/12)

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

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
new .evalute_extent() internal that for fine extent modifications
internal get_spatial_locations_list() and get_spatial_network_list() accessors now accept “:all:” token to get all available, ignoring spat_unit

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()

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

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

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.

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.

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

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

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

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 Use GiottoClass:::.update_giotto_image() to update outdated objects.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

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

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

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

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