### Update Giotto Environment Management Functions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This section details updates to functions responsible for managing the Giotto Python environment, allowing for custom Python installations. New arguments `mini_install_path` and `mini_path` are introduced to support this flexibility in `installGiottoEnvironment()`, `checkGiottoEnvironment()`, and `removeGiottoEnvironment()`.

```APIDOC
installGiottoEnvironment(mini_install_path: str = NULL)
checkGiottoEnvironment(mini_install_path: str = NULL)
removeGiottoEnvironment(mini_path: str = NULL)
```

--------------------------------

### APIDOC: S4 Subobject Basic Generics

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds new basic generics for S4 subobjects, specifically `[]` and `[]<*`. These generics allow for getting or setting information directly into the main data slot of the subobjects, providing intuitive data access and manipulation.

```APIDOC
[]
[]<*
  Purpose: Get or set information in S4 subobject data slot
```

--------------------------------

### APIDOC: Giotto S4 Object Initialization

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces a new `initialize()` generic for Giotto S4 subobjects. This generic automatically calls `setalloccol()` to enable setting by reference for data.table-based S4 subobjects, improving memory management and performance.

```APIDOC
initialize()
  Calls setalloccol() for data.table-based S4 subobjects
```

--------------------------------

### Giotto Object Loading and Saving with Path Expansion

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

The `loadGiotto()` and `saveGiotto()` functions now incorporate `path.expand`, allowing them to correctly interpret and expand provided file and directory paths. This makes file operations more robust and user-friendly across different operating systems.

```APIDOC
loadGiotto(path: str) # path.expand applied
saveGiotto(path: str) # path.expand applied
```

--------------------------------

### Update Giotto Configuration and Parameter Management

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

The `changeGiottoInstructions()` function has been enhanced to allow the addition of new parameters and enforce logical class checking for known parameters. This improves configuration flexibility and robustness, ensuring proper instruction handling.

```APIDOC
changeGiottoInstructions(allow_new_params: bool = TRUE, enforce_logical_class: bool = TRUE)
```

--------------------------------

### APIDOC: System Color Support Detection

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds new system color support detection, based on the logic from the 'crayon' package. This enhances the visual presentation of Giotto outputs by leveraging terminal color capabilities.

```APIDOC
System Color Support Detection
  Based on 'crayon' package logic
```

--------------------------------

### Giotto Object Creation and Data Ingestion Pipeline Updates

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Updates to `createGiottoObject()` introduce a new data ingestion pipeline. This includes modifications to how `cell_ID`, `feat_ID`, `cell_metadata`, and `feat_metadata` slots are initialized, ensuring compatibility with new data structures and improving data handling.

```APIDOC
createGiottoObject(new_data_ingestion_pipeline: bool = TRUE)

# Slot Initialization Modifications:
cell_ID: modified initialization
feat_ID: modified initialization
cell_metadata: modified initialization
feat_metadata: modified initialization
```

--------------------------------

### New Internal Giotto Utilities and Constructors

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Several new internal functions have been added to Giotto for improved data handling and object construction. These include `set_row_order_dt()` for `data.table` ordering, `fread_colmatch()` for subset loading based on column matches, and `create_nn_net_obj()` for `nnNetObj` construction, enhancing internal data management.

```APIDOC
set_row_order_dt(data_table, order_column) # Internal
fread_colmatch(file_path, column_to_match, values_to_match) # Internal
create_nn_net_obj() # Internal constructor for S4 nnNetObj
```

--------------------------------

### Python Package Dependencies (requirements.txt)

Source: https://github.com/drieslab/giotto_website/blob/suite/inst/extdata/giotto_python_modules.txt

Specifies the exact versions of Python packages required for the Giotto website project. This list is typically found in a `requirements.txt` file and is crucial for setting up a consistent and reproducible development and deployment environment.

```Python
pandas==1.1.5
networkx==2.6.3
python-igraph==0.9.6
leidenalg==0.8.7
python-louvain==0.15
python.app==2
scikit-learn==0.24.2
```

--------------------------------

### Relocation of Core Giotto Functions and Objects

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Several core functions, including `create_featureNetwork_object()`, `create_giotto_points_object()`, and `create_giotto_polygon_object()`, have been moved to `classes.R`. The `depth()` function has been relocated from `giotto.R` to `utilities.R` for better modularity and organization.

```APIDOC
# Moved to classes.R:
create_featureNetwork_object()
create_giotto_points_object()
create_giotto_polygon_object()

# Moved to utilities.R:
depth()
```

--------------------------------

### Enhanced Parameter Flexibility and Package Check Options

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

The `polyStamp()` function gains `id_col`, `x_col`, and `y_col` parameters for more flexible stamp location input, improving its adaptability. The `package_check()` function now includes `optional` and `custom_msg` parameters, allowing for more nuanced and informative package dependency checks.

```APIDOC
polyStamp(id_col: str = NULL, x_col: str = NULL, y_col: str = NULL)
package_check(package_name: str, optional: bool = FALSE, custom_msg: str = NULL)
```

--------------------------------

### Clustering and Data Conversion Bug Fixes

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Bugs in `doLouvainCluster()` subfunctions have been resolved, making them compatible with the new Giotto Suite framework. Additionally, `gefToGiotto()` has received a fix for its `bin_size` arguments, ensuring correct data conversion from Stereo*seq GEF files.

```APIDOC
doLouvainCluster(giotto_suite_compatible: bool = TRUE)
gefToGiotto(bin_size_args_fixed: bool = TRUE)
```

--------------------------------

### APIDOC: Load 10x Xenium Data into Giotto

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces `createGiottoXeniumObject()` for loading 10x Xenium data. This new function facilitates the integration of Xenium spatial transcriptomics data into the Giotto analysis pipeline.

```APIDOC
createGiottoXeniumObject()
```

--------------------------------

### New GiottoData Package for Spatial Datasets (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces the `GiottoData` package designed to manage spatial datasets within the Giotto framework. This package centralizes preprocessed Giotto objects (minidatasets) and now hosts previously standalone functions like `getSpatialDataset()` and `loadGiottoMini()` for improved data organization and accessibility.

```APIDOC
Package: GiottoData
Description: New package to work with spatial datasets associated with Giotto.
  - Stores minidatasets: preprocessed giotto objects ready for use.
  - Moved functions: getSpatialDataset(), loadGiottoMini()
```

--------------------------------

### APIDOC: Show Functions Display Update

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Updates `show` functions to display color-coded nesting names and a tree structure. This enhances the visual representation of Giotto objects, making their hierarchical structure more intuitive to understand.

```APIDOC
show() functions
  Updated to display color-coded nesting names and tree structure
```

--------------------------------

### Breaking Changes in Giotto 3.2.0

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Giotto 3.2.0 introduces several breaking changes to improve consistency and functionality. These include the removal of deprecated `@nn_network` nesting, a default output change for `createSpatialNetwork()` to `spatialNetworkObj`, and setting incomplete classes as virtual to prevent unintended instantiation. Additionally, certain `createGiottoCosMxObject()` workflows have been temporarily removed for updates.

```APIDOC
# Deprecated:
@nn_network slot nesting

# createSpatialNetwork() output change:
createSpatialNetwork(return_gobject: bool = FALSE, output: str = 'spatialNetworkObj') # Default output changed

# Class Instantiation:
Incomplete classes set as virtual

# Removed Workflows:
createGiottoCosMxObject(aggregate_workflow: bool = FALSE, all_workflow: bool = FALSE)
```

--------------------------------

### APIDOC: Update createGiottoCosMxObject

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Updates `createGiottoCosMxObject()` for Giotto 3.0 and modularization. The subcellular workflow has been tested and updated, along with an accompanying tutorial, to ensure compatibility and improved functionality.

```APIDOC
createGiottoCosMxObject()
  Updated for Giotto 3.0 and modularization
```

--------------------------------

### New Giotto Object Save and Load Functions (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces `saveGiotto()` and `loadGiotto()` functions for robust preservation and retrieval of Giotto objects. These functions are wrappers around `saveRDS()` and `readRDS()`, specifically enhanced to handle memory-pointer based objects like `spatVector` and `spatRaster`, ensuring proper serialization of complex Giotto structures.

```APIDOC
Function: saveGiotto(giotto_object, folder_path)
Description: Saves a Giotto object into a specified folder using a specific structure. Works with spatVector and spatRaster pointers.

Function: loadGiotto(folder_path)
Description: Loads a Giotto object from a specified folder.
```

--------------------------------

### APIDOC: New S4 Subobjects Framework

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces new S4 subobjects, detailed in `classes.R`. This framework enhances the modularity and organization of Giotto objects, improving data management and extensibility.

```APIDOC
S4 Subobjects Framework
  Details in classes.R
```

--------------------------------

### APIDOC: Convert Scanpy Anndata to Giotto

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds `anndataToGiotto()` to convert scanpy anndata objects to Giotto objects. This function improves interoperability, allowing users to seamlessly transfer data between Scanpy and Giotto frameworks.

```APIDOC
anndataToGiotto()
```

--------------------------------

### General Function Argument and Behavior Updates

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This section details updates to existing Giotto functions, including changes to arguments for increased flexibility, modifications to default parameters, and overhauls of object creation functions to align with new data structures or processing workflows.

```APIDOC
runWNN(giotto_object, ...):
  Arguments updated to handle any number of modalities, enhancing function flexibility.

runIntegratedUMAP(giotto_object, ...):
  Arguments updated to handle any number of modalities, enhancing function flexibility.

jackstrawPlot(giotto_object, scaling, centering, feats_to_use, ...):
  Updated for greater flexibility and efficiency. Default parameters for 'scaling', 'centering', and 'feats_to_use' now match 'runPCA()'.

runtSNE(giotto_object, reduction, ...):
  Changed warning to error when 'reduction' is 'feats' to prevent accidental wiping of the giotto object.

screePlot(giotto_object, name, ...):
  'name' parameter deprecated in favor of 'dim_reduction_name'.

createGiottoXeniumObject(spatial_locs, ...):
  Function has been overhauled, and its parameters have changed significantly.

createGiottoVisiumObject(spatial_locs, do_manual_adj, image_adjustment_params, ...):
  'do_manual_adj' and image adjustment parameters removed. This function now creates a 'giottoLargeImage' for spatial images.

exprCellCellcom(giotto_object, gene_set_1, gene_set_2, ...):
  Deprecated 'gene_set_*' parameters have been removed.

findNetworkNeighbors(giotto_object, spatial_network_name, ...):
  Default value for 'spatial_network_name' is now 'NULL'.

get10Xmatrix(path, split_by_type, ...):
  Now correctly obeys the 'split_by_type = FALSE' parameter.
```

--------------------------------

### Giotto CosMx Object and Plotting Enhancements

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Bug fixes and updates have been applied to `createGiottoCosMxObject()` concerning polygon placement and generation. The `plot()` method for `giottoPoints` now defaults to a faster rasterized plotting option, significantly improving visualization performance for large datasets.

```APIDOC
createGiottoCosMxObject(polygon_placement_fixed: bool = TRUE)
plot(giottoPoints_object, rasterized: bool = TRUE) # rasterized now default
```

--------------------------------

### Enhancements to Existing Functions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This section describes improvements and new options added to existing Giotto functions, enhancing their functionality or user experience.

```APIDOC
normalizeGiotto(giotto_object, method, ...):
  Added 'quantile' normalization method.

print(object):
  New 'print()' methods implemented for 'icfObject' and 'combIcfObject'.

readPolygonVizgenParquet(path, calc_centroids, ...):
  'calc_centroids' parameter now defaults to 'TRUE'.
```

--------------------------------

### New Giotto Interoperability Functions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Giotto 3.2.0 introduces new functions for enhanced interoperability with other single-cell analysis ecosystems. This includes `gefToGiotto()` for Stereo*seq GEF objects, `giottoToAnnData()` for squidpy/AnnData .h5ad files, and `giottoToSpatialExperiment()` with its counterpart `spatialExperimentToGiotto()` for seamless conversion with SpatialExperiment objects.

```APIDOC
gefToGiotto(gef_object)
giottoToAnnData(giotto_object) # Converts to .h5ad
giottoToSpatialExperiment(giotto_object)
spatialExperimentToGiotto(spatial_experiment_object)
```

--------------------------------

### New Polygon Shape Array Creation Functions (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces `polyStamp()`, `circleVertices()`, and `rectVertices()` for programmatic creation of polygon shape arrays. These functions facilitate the generation of custom geometric shapes, useful for spatial analysis and data manipulation within Giotto.

```APIDOC
Function: polyStamp()
Description: Creates polygon shape arrays.

Function: circleVertices()
Description: Generates vertices for circular shapes.

Function: rectVertices()
Description: Generates vertices for rectangular shapes.
```

--------------------------------

### New Functions and Major Features

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This section highlights newly introduced functions and significant features added to the Giotto package, expanding its capabilities in spatial data analysis, label transfer, and image processing.

```APIDOC
identifyTMAcores(giotto_object, ...):
  New function for assigning IDs to tissue microarray spatial data.

labelTransfer(giotto_object_source, giotto_object_target, ...):
  New function for transferring labels between giotto objects or subsets thereof. Supercedes 'doClusterProjection()'.

Dataset Affine Registration:
  Implemented via an interactive shiny app and automated SIFT detection.

Cell Segmentation:
  New capability for cell segmentation via Cellpose.

read10xAffineImage(path, ...):
  New function for reading 10x affine transformed images.

Modular Importer and Convenience Functions:
  Several new modular importer and convenience functions have been added.

ONTraC Implementation:
  New implementation of ONTraC.

interpolateFeature(giotto_object, ...):
  New function for kriging interpolation of values.
```

--------------------------------

### APIDOC: Seed Setting Behavior Update

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Updates seed setting behavior in `dimension_reduction.R` and `clustering.R`. This change likely improves reproducibility and consistency of results in dimension reduction and clustering analyses.

```APIDOC
Seed Setting Behavior
  Updated in dimension_reduction.R and clustering.R
```

--------------------------------

### New Giotto Object Generics and Methods

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Giotto 3.2.0 introduces a suite of new generics and methods for enhanced manipulation of Giotto objects and their subobjects. This includes `wrap()`, `vect()`, `rotate()`, `t()`, `spatShift` for spatial manipulation, and accessors like `spatIDs()`, `featIDs()`, `objName()`, and `rbind()` for `giottoPolygon` objects, providing greater programmatic control.

```APIDOC
# New Generics:
wrap(giotto_object)
vect(giotto_object)
rotate(giotto_subobject, angle: numeric)
t(giotto_subobject) # Transpose
spatShift(giotto_subobject, x_shift: numeric, y_shift: numeric)
sp
```

--------------------------------

### APIDOC: Unicode Character Printing Update

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Updates Unicode character printing with `show` functions for Latin1 systems. This improves compatibility and display of special characters across different system configurations.

```APIDOC
show() functions
  Updated Unicode character printing for Latin1 systems
```

--------------------------------

### APIDOC: Giotto S4 Subobject Slot Accessors

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds new `spatUnit`, `spatUnit<*`, `featType`, and `featType<*` generics for S4 subobjects. These generics provide standardized methods for setting the relevant spatial unit and feature type slots within Giotto's S4 object structure.

```APIDOC
spatUnit()
spatUnit<*()
featType()
featType<*()
  Purpose: Set relevant slots for S4 subobjects
```

--------------------------------

### Dependency and Package Requirements Updates

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This section details changes in package dependencies and version requirements for Giotto and its associated packages, ensuring compatibility and proper functionality.

```APIDOC
Dependency Changes (Giotto 4.1.2):
  - 'limma', 'plotly', and 'Rtsne' moved to Suggests.
  - 'progressr' and 'jsonlite' dependencies moved to GiottoUtils v0.1.12.
  - 'reshape2' dependency removed.

Dependency Requirements (Giotto 4.1.0):
  - Requires GiottoUtils (>= 0.1.10).
  - Requires GiottoClass (>= 0.3.3).

Dependency Requirements (Giotto 4.0.8):
  - Requires GiottoVisuals (>= 0.2.2).
  - Requires GiottoClass (>= 0.3.1).
  - Requires GiottoUtils (>= 0.1.8).

Dependency Requirements (Giotto 4.0.6):
  - Requires GiottoVisuals (>= 0.2.0).
  - Requires GiottoClass (>= 0.3.0).
```

--------------------------------

### New Plotting and Visualization Parameters

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Giotto 3.2.0 enhances plotting capabilities with new parameters for finer control over visualizations. `coord_fix_ratio` is added to `spatFeatPlot2D()` and `spatFeatPlot2D_single()`, and an `order` parameter is introduced to `dimFeatPlot2D` and `spatDimFeatPlot2d` for plotting and ordering cells based on selected feature levels.

```APIDOC
spatFeatPlot2D(coord_fix_ratio: bool = FALSE)
spatFeatPlot2D_single(coord_fix_ratio: bool = FALSE)
dimFeatPlot2D(order: str = NULL) # Order cells by feature levels
spatDimFeatPlot2d(order: str = NULL) # Order cells by feature levels
```

--------------------------------

### APIDOC: Fix joinGiottoObjects Metadata Bug

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Fixes a bug in `joinGiottoObjects()` related to metadata processing. This ensures accurate and consistent metadata handling when combining Giotto objects.

```APIDOC
joinGiottoObjects()
  Bug fix in metadata processing
```

--------------------------------

### APIDOC: Grid Plotting Default Columns

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Updates grid plotting behavior to automatically set a default number of columns based on the elements to plot. This default can be overridden by explicitly providing input to the `cow_n_col` parameter, offering more flexible visualization control.

```APIDOC
Grid Plotting Behavior
  Default columns set based on elements
  Override with param: cow_n_col
```

--------------------------------

### Expression Data Reading and Evaluation Compatibility

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

The `read_expression_data()` and `evaluate_expr_matrix()` functions have been updated to ensure full compatibility with the new `exprObj` structure. This streamlines expression data processing within Giotto, making it more robust and efficient.

```APIDOC
read_expression_data(compatible_with_exprObj: bool = TRUE)
evaluate_expr_matrix(compatible_with_exprObj: bool = TRUE)
```

--------------------------------

### Deprecated Arguments and Behaviors in Specific Functions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This snippet details specific arguments or behaviors that have been deprecated within existing Giotto functions, often due to changes in underlying methodologies or external package integrations.

```APIDOC
runGiottoHarmony(giotto_object, do_pca, expression_values, feats_to_use, ...):
  'do_pca', 'expression_values', and 'feats_to_use' arguments have been removed. Running PCA during the 'harmony::RunHarmony()' call is now deprecated.
```

--------------------------------

### Bug Fixes Across Giotto Versions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This section lists various bug fixes implemented across different Giotto versions, addressing issues ranging from plotting errors and data processing glitches to metadata handling and parameter passing.

```APIDOC
processGiotto(giotto_object, ...):
  Can now skip the adjust step by default.

Xenium Convenience Functions:
  Allow 'giottoInstructions' passing.

plotInteractivePolygons(giotto_object, ...):
  Fixed error when providing a spatial plot with a continuous scale (Issue #964).

DWLS find_dampening_constant(S, ...):
  Fixed error when 'S[subset, ]' produces only 1 gene.

interpolateFeatures(giotto_object, ...):
  Fixed error where feature names with '-' or starting with numbers did not work.

runPCAprojectionBatch(giotto_object, ncp, ...):
  Added a catch for when 'ncp' requested exceeds the number of features used.

spatCellCellcom(giotto_object, verbose, ...):
  Now respects the 'verbose' flag (Issue #949).

binSpect(giotto_object, ...):
  Fixed parameter passing error introduced in v4.0.6.

viewHMRFresults3D(giotto_object, ...):
  Updated.

viewHMRFresults2D(giotto_object, ...):
  Updated.

createCrossSections(giotto_object, ...):
  Updated.

insertCrossSectionSpatPlot3D(giotto_object, ...):
  Updated.

crossSectionPlot(giotto_object, ...):
  Updated.

crossSectionFeatPlot3D(giotto_object, ...):
  Updated.

insertCrossSectionFeatPlot3D(giotto_object, ...):
  Updated.

crossSectionPlot3D(giotto_object, ...):
  Updated.

crossSectionFeatPlot(giotto_object, ...):
  Updated.

spatialDE(giotto_object, ...):
  Fixed Error "cannot coerce class ‘structure("spatLocsObj", package = "Giotto")’ to a data.frame".

Metadata Handling (addHMRF, addFeatsPerc, doScrubletDetect):
  Fixed metadata appending/sorting issues introduced by GiottoClass v0.1.3 (2024/01/12).
```

--------------------------------

### New Accessor Functions for Cell and Feature Metadata (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds new accessor functions `get_CellMetadata()`, `set_CellMetadata()`, `get_FeatMetadata()`, and `set_FeatMetadata()` for standardized retrieval and modification of cell and feature metadata. These functions provide clearer interfaces, with `get_CellMetadata()` and `get_FeatMetadata()` serving as aliases for `pDataDT()` and `fDataDT()` respectively.

```APIDOC
Function: get_CellMetadata()
Alias: pDataDT()
Description: Retrieves cell metadata.

Function: set_CellMetadata()
Description: Sets cell metadata.

Function: get_FeatMetadata()
Alias: fDataDT()
Description: Retrieves feature metadata.

Function: set_FeatMetadata()
Description: Sets feature metadata.
```

--------------------------------

### APIDOC: Aggregate Stacks Functions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces `aggregateStacks()` set of functions. These functions are designed to work with multiple subcellular layers when generating aggregated expression matrices, enabling multi-layer spatial analysis.

```APIDOC
aggregateStacks() set of functions
  Purpose: Work with multiple subcellular layers for aggregated expression matrices
```

--------------------------------

### APIDOC: Setter Functions Update

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Updates `setter` functions to read the `@spat_unit` and `@feat_type` slots of subobjects. This determines nesting, ensuring correct data organization and manipulation within the Giotto object structure.

```APIDOC
setter functions
  Updated to read @spat_unit and @feat_type slots for nesting
```

--------------------------------

### APIDOC: S4 Subobjects Framework Requirement

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

The new S4 subobjects framework is a breaking change, requiring existing Giotto objects to be remade. This fundamental change improves object structure and management but necessitates data re-processing.

```APIDOC
S4 Subobjects Framework
  Requires Giotto objects to be remade
```

--------------------------------

### Internal Giotto Function Refactoring and Organization

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Internal functions have been reorganized across `giotto.R`, `data_evaluation.R`, and `data_input.R`. This includes new slot `check` functions for object consistency, `evaluate` functions for data wrangling, and `read` functions for data ingestion, improving code structure and maintainability.

```APIDOC
# giotto.R:
check_gobject_consistency() # new/refactored slot check functions

# data_evaluation.R:
evaluate_external_data() # new/refactored evaluate functions

# data_input.R:
read_data_to_giotto_subobjects() # new/refactored read functions

# dd.R:
dummy_documentation_inheritance()
```

--------------------------------

### APIDOC: Fix annotateGiotto Bug

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Fixes a bug in `annotateGiotto()` that occurred after the 3.0 update. This ensures correct annotation functionality within the Giotto framework.

```APIDOC
annotateGiotto()
  Bug fix after 3.0 update
```

--------------------------------

### APIDOC: S4 Subobject Provenance Slot

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds a new `@provenance` slot to S4 subobjects. This slot tracks the provenance of aggregated information, such as `z_layers` used, ensuring data traceability and reproducibility.

```APIDOC
@provenance slot
  Purpose: Track provenance of aggregated information (e.g., z_layers)
```

--------------------------------

### APIDOC: Calculate Overlap Polygon Images

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces `calculateOverlapPolygonImages()` for calculating overlapped intensities from image-based information (e.g., IMC, IF, MIBI) and polygon data (e.g., cell). This is crucial for integrating imaging and spatial data.

```APIDOC
calculateOverlapPolygonImages()
  Purpose: Calculate overlapped intensities from image and polygon data
```

--------------------------------

### New Spatial Autocorrelation Analysis Functions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

New functions `spatialAutoCorLocal()` and `spatialAutoCorGlobal()` are added to identify spatial autocorrelations from expression and cell metadata. A new utility, `createSpatialWeightMatrix()`, is also introduced to generate spatial weight matrices from spatial networks, which are essential for these autocorrelation analyses.

```APIDOC
spatialAutoCorLocal(expression_data, cell_metadata)
spatialAutoCorGlobal(expression_data, cell_metadata)
createSpatialWeightMatrix(spatial_network_object)
```

--------------------------------

### Function Deprecations and Replacements (Enrichment and Spatial Correlation)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

This section outlines functions that have been deprecated or removed, providing their recommended replacements. This primarily affects enrichment analysis functions and functions dealing with spatial correlation of 'Genes', which are now generalized to 'Feats'.

```APIDOC
PAGEEnrich(): Deprecated. Use runPAGEEnrich() instead.
rankEnrich(): Deprecated. Use runRankEnrich() instead.
hyperGeometricEnrich(): Deprecated. Use runHyperGeometricEnrich() instead.
createSpatialEnrich(): Deprecated. Use runSpatialEnrich() instead.
runPAGEEnrich_OLD(): Deprecated. Use runPAGEEnrich() instead.

heatmSpatialCorGenes(): Deprecated. Use heatmSpatialCorFeats() instead.
detectSpatialCorGenes(): Removed. Use detectSpatialCorFeats() instead.
findInteractionChangedGenes(): Removed. Use findInteractionChangedFeats() instead.
findCellProximityGenes(): Removed. Use findInteractionChangedFeats() instead.

crossSectionGenePlot(): Removed. Use crossSectionFeatPlot() instead.
crossSectionGenePlot3D(): Removed. Use crossSectionFeatPlot3D() instead.
insertCrossSectionGenePlot3D(): Removed. Use insertCrossSectionFeatPlot3D() instead.
```

--------------------------------

### APIDOC: Disable Colored Text in Show Functions

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds the ability to turn off colored text in `show` functions by setting `options("giotto.color_show" = FALSE)`. This provides users with control over the display format of Giotto objects.

```APIDOC
options("giotto.color_show" = FALSE)
  Purpose: Disable colored text in show functions
```

--------------------------------

### APIDOC: Convert Overlap to Expression Matrix

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds `overlapImagesToMatrix()`, which converts intensity-polygon overlap information into an expression matrix (e.g., cell by protein). This function facilitates the transformation of spatial imaging data into a quantitative matrix format for downstream analysis.

```APIDOC
overlapImagesToMatrix()
  Purpose: Convert intensity-polygon overlap to expression matrix
```

--------------------------------

### New Filter Distributions Function (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Introduces `filterDistributions()` to generate histogram plots from expression statistics. This function aids in visualizing and understanding the distribution of expression data, facilitating data quality control and analysis.

```APIDOC
Function: filterDistributions()
Description: Generates histogram plots from expression statistics.
```

--------------------------------

### APIDOC: Python Version Update Requirement

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

A breaking change requiring an update of the Python version to 3.10.2. This ensures compatibility with Giotto Suite 2.1.0 and may require users to update their Python environments.

```APIDOC
Python Version Update
  Required: 3.10.2
```

--------------------------------

### New Interactive Polygon Plotting Function (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds `plotInteractivePolygon()` to enable interactive polygonal selection of points directly within plots. This function enhances user interaction for data exploration and selection based on spatial regions.

```APIDOC
Function: plotInteractivePolygon()
Description: Enables interactive polygonal selection of points within a plot.
```

--------------------------------

### Breaking Change: ICF Output Structure Renamed (Giotto API)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

A breaking change has been introduced where the internal object structure names for ICF (Interaction Changed Features) output have been updated. The term 'genes' has been replaced with 'feats' to reflect a broader applicability beyond just gene-centric analysis, requiring adjustments in code that directly accesses these internal structures.

```APIDOC
ICF Output Structure:
  - Old internal object structure names used 'genes'
  - New internal object structure names use 'feats'
```

--------------------------------

### APIDOC: Fix extract_polygon_list Bug

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Fixes a bug in `extract_polygon_list()`. This ensures correct extraction of polygon lists, which is crucial for spatial data handling.

```APIDOC
extract_polygon_list()
  Bug fix
```

--------------------------------

### Deprecated Combine Functions for Interaction Changed Genes (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Functions designed to combine 'Interaction Changed Genes' data have been deprecated. The new 'Features' functions should be used instead to combine interaction-related data, reflecting the standardized API terminology.

```APIDOC
Deprecated: combineInteractionChangedGenes(), combineICG(), combineCPG()
Replaced by: combineInteractionChangedFeats(), combineICF()
```

--------------------------------

### Deprecated Plotting Functions for Interaction Changed Genes (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Several plotting functions related to 'Interaction Changed Genes' have been deprecated to standardize terminology and improve consistency across the Giotto API. Users should now use the 'Features' counterparts for plotting interaction-related data, aligning with broader applicability beyond just gene-centric analysis.

```APIDOC
Deprecated: plotInteractionChangedGenes(), plotICG(), plotCPG()
Replaced by: plotInteractionChangedFeatures(), plotICF(), plotCPF()
```

--------------------------------

### APIDOC: Hexagonal Vertices Generation

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Adds `hexVertices()` to the polygon shape array generation functionality. This function is used for creating hexagonal vertex data, likely for spatial visualization or analysis.

```APIDOC
hexVertices()
```

--------------------------------

### Deprecated Combine Cell Proximity Genes per Interaction Function (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

The `combineCellProximityGenes_per_interaction()` function has been deprecated as part of the API's terminology standardization. Users should now use `combineCellProximityFeatures_per_interaction()` for equivalent functionality, which adopts the more general 'Features' nomenclature.

```APIDOC
Deprecated: combineCellProximityGenes_per_interaction()
Replaced by: combineCellProximityFeatures_per_interaction()
```

--------------------------------

### Deprecated Combine Plotting Functions for Interaction Changed Genes (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

A set of functions for combining plots of 'Interaction Changed Genes' has been deprecated to align with the new 'Features' terminology. Users should now use the corresponding 'Features' functions for combining interaction-related plots, ensuring consistency with updated API standards.

```APIDOC
Deprecated: plotCombineInteractionChangedGenes(), plotCombineICG(), plotCombineCPG()
Replaced by: plotCombineInteractionChangedFeatures(), plotCombineICF()
```

--------------------------------

### Deprecated Filter Functions for Interaction Changed Genes (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Functions for filtering 'Interaction Changed Genes' have been deprecated. Users should now utilize the 'Features' counterparts to filter interaction-related data, ensuring adherence to the updated API terminology and improved consistency.

```APIDOC
Deprecated: filterInteractionChangedGenes(), filterICG(), filterCPG()
Replaced by: filterInteractionChangedFeats(), filterICF()
```

--------------------------------

### Deprecated Find Functions for Interaction Changed Genes (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

Functions used to find 'Interaction Changed Genes' have been deprecated in favor of new functions that use the more general 'Features' terminology. This change promotes API consistency and broader applicability of analysis results.

```APIDOC
Deprecated: findInteractionChangedGenes(), findICG(), findCPG()
Replaced by: findInteractionChangedFeats(), findICF()
```

--------------------------------

### Deprecated Plot Cell Proximity Genes Function (R/APIDOC)

Source: https://github.com/drieslab/giotto_website/blob/suite/NEWS.md

The `plotCellProximityGenes()` function has been deprecated as part of an effort to standardize API terminology. Users should transition to `plotCellProximityFeatures()` for equivalent functionality, which uses a more general 'Features' nomenclature.

```APIDOC
Deprecated: plotCellProximityGenes()
Replaced by: plotCellProximityFeatures()
```

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