3.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 3.0.1
+Version: 3.1
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre")),

NAMESPACE

@@ -136,6 +136,7 @@ export(estimateImageBg)
 export(exportGiottoViewer)
 export(exprCellCellcom)
 export(fDataDT)
+export(featType)
 export(featureNetwork)
 export(fiji)
 export(filterCPG)
@@ -169,6 +170,7 @@ export(getCellsFromPolygon)
 export(getClusterSimilarity)
 export(getDendrogramSplits)
 export(getDistinctColors)
+export(getGEFtxCoords)
 export(get_NearestNetwork)
 export(get_dimReduction)
 export(get_expression_values)
@@ -188,6 +190,7 @@ export(giottoToSeurat)
 export(giottoToSpatialExperiment)
 export(heatmSpatialCorFeats)
 export(heatmSpatialCorGenes)
+export(hexVertices)
 export(hyperGeometricEnrich)
 export(insertCrossSectionGenePlot3D)
 export(insertCrossSectionSpatPlot3D)
@@ -245,6 +248,7 @@ export(plotUMAP_3D)
 export(plot_spat_voronoi_layer_ggplot)
 export(polyStamp)
 export(processGiotto)
+export(prov)
 export(rankEnrich)
 export(rankSpatialCorGroups)
 export(readExprMatrix)
@@ -349,6 +353,7 @@ export(spatNetwDistributionsKneighbors)
 export(spatPlot)
 export(spatPlot2D)
 export(spatPlot3D)
+export(spatUnit)
 export(spatialAEH)
 export(spatialDE)
 export(specificCellCellcommunicationScores)
@@ -389,11 +394,17 @@ exportMethods("$")
 exportMethods("$<-")
 exportMethods("[")
 exportMethods("[<-")
+exportMethods("featType<-")
+exportMethods("prov<-")
+exportMethods("spatUnit<-")
 exportMethods(copy)
 exportMethods(dim)
+exportMethods(featType)
 exportMethods(ncol)
 exportMethods(nrow)
 exportMethods(plot)
+exportMethods(prov)
+exportMethods(spatUnit)
 import(data.table)
 import(ggplot2)
 import(magrittr)

NEWS.md

@@ -0,0 +1,104 @@
+# Giotto Suite 3.1.0 (2202-12-01)  
+
+
+## Added
+- New `initialize()` generic that calls `setalloccol()` for data.table-based S4 subobjects to allow setting by reference
+- New `spatUnit`, `spatUnit<-`, `featType`, and `featType<-` feat type generics for S4 subobjects for setting the relevant slots
+- Add `hexVertices()` to polygon shape array generation functionality
+
+## Changes  
+- Update `createGiottoCosMxObject()` for 3.0 and modularization of functions. 'subcellular' workflow has been tested to work along with an updated tutorial.
+- Update grid plotting behavior to set a default number columns to use based on number of elements to plot. Can be overridden by explicitly providing input to `cow_n_col` param
+- Fix bug in `annotateGiotto()` after 3.0 update ([#433](https://github.com/drieslab/Giotto/issues/433#issuecomment-1324211224))
+- Fix bug in `joinGiottoObjects()` metadata processing
+- Update seed setting behavior in [dimension_reduction.R](https://github.com/drieslab/Giotto/blob/suite/R/dimension_reduction.R) and [clustering.R](https://github.com/drieslab/Giotto/blob/suite/R/clustering.R)
+
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+
+
+# Giotto Suite 3.0.1 (2022-11-20)
+
+## Added
+- New system color support detection (based on crayon package logic)
+- Add ability to turn off colored text in `show` functions with `options("giotto.color_show" = FALSE)`
+
+## Changes
+- Fix bug in `extract_polygon_list()` ([#433](https://github.com/drieslab/Giotto/issues/433#issuecomment-1321221382))
+- Update Unicode character printing with `show` functions for Latin1 systems
+
+
+
+
+
+# Giotto Suite 3.0.0 (2022-11-18)
+
+## Breaking Changes
+- S4 subobjects framework will require giotto objects to be remade
+
+## Added
+- New `createGiottoXeniumObject()` for loading 10x Xenium data
+- New S4 subobjects. Details can be found in [classes.R](https://github.com/drieslab/Giotto/blob/suite/R/classes.R)
+- New basic generics for S4 subobjects. Mainly the use of `[]` and `[]<-` to get or set information into the main data slot
+- New `@provenance` slot in S4 subobjects to track provenance of aggregated information (z_layers used for example)
+- New `calculateOverlapPolygonImages()` for calculating overlapped intensities from image-based information (e.g. IMC, IF, MIBI, ...) and polygon data (e.g. cell)
+- New `overlapImagesToMatrix()` converts intensity-polygon overlap info into an expression matrix (e.g. cell by protein)
+- New `aggregateStacks()` set of functions work with multiple subcellular layers when generating aggregated expression matrices
+
+## Changes
+- Update `setter` functions to read the `@spat_unit` and `@feat_type` slots of subobjects to determine nesting
+- Update of `show` functions to display color coded nesting names and tree structure
+
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+
+
+# Giotto Suite 2.1.0 (2202-11-09)
+
+## Breaking Changes
+- Update of python version to **3.10.2** [details](https://giottosuite.readthedocs.io/en/latest/additionalinformation.html#id1)
+
+## Added
+- New `anndataToGiotto()` to convert scanpy anndata to Giotto [details](https://giottosuite.readthedocs.io/en/latest/additionalinformation.html#id2)
+
+
+
+
+
+
+# Giotto Suite 2.0.0.998
+
+## Added
+- New `GiottoData` package to work with spatial datasets associated with Giotto
+	- Stores the minidatasets: preprocessed giotto objects that are ready to be used in any function
+	- Moved: `getSpatialDataset()` and `loadGiottoMini()` functions to this package
+- New `saveGiotto()` and `loadGiotto()` for preserving memory-pointer based objects. In [general_help.R](https://github.com/drieslab/Giotto/blob/suite/R/general_help.R)
+  - It saves a Giotto object into a folder using a specific structure. Essentially a wrapper around `saveRDS()` that also works with spatVector and spatRaster pointers.
+- New `plotInteractivePolygon()` for plot-interactive polygonal selection of points.
+- New polygon shape array creation through `polyStamp()`, `circleVertices`, `rectVertices`. In [giotto_structures.R](https://github.com/drieslab/Giotto/blob/suite/R/giotto_structures.R)
+- Add accessor functions `get_CellMetadata` (alias of `pDataDT()`), `set_CellMetadata`, `get_FeatMetadata` (alias of `fDataDT()`), `set_FeatMetadata`. See [accessors.R](https://github.com/drieslab/Giotto/blob/suite/R/accessors.R)
+- New `filterDistributions()` to generate histogram plots from expression statistics
+
+## Changes
+- Deprecate `plotInteractionChangedGenes()` ,`plotICG()`, `plotCPG()` in favor of `plotInteractionChangedFeatures()` and `plotICF()` and `plotCPF()`
+- Deprecate `plotCellProximityGenes()`, in favor of `plotCellProximityFeatures()`
+- Deprecate `plotCombineInteractionChangedGenes()`, `plotCombineICG()`, `plotCombineCPG()` in favor of `plotCombineInteractionChangedFeatures()` and `plotCombineICF()`
+- Deprecate `findInteractionChangedGenes()`, `findICG()`, `findCPG()` in favor of `findInteractionChangedFeats()` and `findICF`
+- Deprecate `filterInteractionChangedGenes()`, `filterICG()`, `filterCPG()` in favor of `filterInteractionChangedFeats()` and `filterICF()`
+- Deprecate `combineInteractionChangedGenes()`, `combineICG()`, `combineCPG()` in favor of `combineInteractionChangedFeats()` and `combineICF()`
+- Deprecate `combineCellProximityGenes_per_interaction()` in favor of `combineCellProximityFeatures_per_interaction()`
+
+## Breaking Changes
+- ICF output internal object structure names have changed to use feats instead of genes
+
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