chore: update doc page

_pkgdown.yml

@@ -623,11 +623,19 @@ reference:
   - GiottoClass::showProcessingSteps
   - GiottoClass::calculateMetaTable
   - GiottoClass::calculateMetaTableCells
-  - GiottoClass::combineMetadata
   - GiottoClass::createMetafeats
   - findNetworkNeighbors
   - GiottoClass::objHistory
   - fiji
+- title: Report Extractors
+  desc: Functions to extract report tables of information
+- contents:
+  - GiottoClass::spatValues
+  - GiottoClass::combineCellData
+  - GiottoClass::combineFeatureData
+  - GiottoClass::combineMetadata
+  - GiottoClass::combineSpatialCellMetadataInfo
+  - GiottoClass::combineFeatureOverlapData
 - title: Giotto Getters & Setters
   desc: Low level functions to get, set and show Giotto slots.
 - contents:
@@ -754,16 +762,6 @@ reference:
   - findScranMarkers_one_vs_all
   - findMastMarkers
   - findMastMarkers_one_vs_all
-- title: Auxiliary Visualizations
-  desc: Functions for different visualization options to explore gene, cell or cluster characteristics.
-- contents:
-  - GiottoVisuals::showClusterHeatmap()
-  - GiottoVisuals::showClusterDendrogram
-  - GiottoVisuals::plotHeatmap
-  - GiottoVisuals::plotMetaDataHeatmap
-  - GiottoVisuals::plotMetaDataCellsHeatmap
-  - GiottoVisuals::violinPlot
-  - callSpdep
 - title: Spatial Enrichment
   desc: Algorithms to compute spatial enrichment of gene signatures or scRNA-seq matrix.
 - contents:
@@ -832,10 +830,6 @@ reference:
   - showSpatialCorGenes
   - rankSpatialCorGroups
   - getBalancedSpatCoexpressionFeats
-- title: Spatial Data Handling
-  desc: Functions to condense spatial data.
-- contents:
-  - GiottoClass::combineSpatialCellMetadataInfo
 - title: Hidden Markov Random Field (HMRF)
   desc: Functions to identify spatial domains with HMRF.
 - contents:
@@ -851,11 +845,16 @@ reference:
   - viewHMRFresults
   - viewHMRFresults2D
   - viewHMRFresults3D
-- title: General Plotting
-  desc: Functions to assist in plotting.
+- title: Basic Visualizations
+  desc: Functions for different visualization options to explore gene, cell or cluster characteristics.
 - contents:
-  - GiottoVisuals::getDistinctColors
-  - GiottoVisuals::showSaveParameters
+  - GiottoVisuals::showClusterHeatmap()
+  - GiottoVisuals::showClusterDendrogram
+  - GiottoVisuals::plotHeatmap
+  - GiottoVisuals::plotMetaDataHeatmap
+  - GiottoVisuals::plotMetaDataCellsHeatmap
+  - GiottoVisuals::violinPlot
+  - GiottoVisuals::dotPlot
 - title: 2D Visualization In Expression Space
   desc: Visualization of expression space (e.g. UMAP) in 2D.
 - contents:
@@ -895,6 +894,13 @@ reference:
   desc: Visualization in 3D spatial space.
 - contents:
   - GiottoVisuals::spatDimPlot3D
+- title: Plotting Utilities
+  desc: Functions to assist in plotting.
+- contents:
+  - GiottoUtils::getDistinctColors
+  - GiottoUtils::getRainbowColors
+  - GiottoVisuals::getColors
+  - GiottoVisuals::showSaveParameters
 - title: In Silico Cross Sections
   desc: Functions to create an in silico 2D cross sections from 3D data.
 - contents:
@@ -983,9 +989,6 @@ reference:
   - GiottoClass::calculateOverlapPolygonImages
   - GiottoClass::calculateOverlapRaster
   - GiottoClass::calculateOverlapSerial
-  - GiottoClass::combineCellData
-  - GiottoClass::combineFeatureData
-  - GiottoClass::combineFeatureOverlapData
   - GiottoClass::createGiottoPoints
   - GiottoClass::createGiottoPolygon
   - GiottoClass::overlapToMatrix
@@ -1053,6 +1056,10 @@ reference:
   - plotSpatNicheClusterBin
   - plotSpatNicheClusterProb
   - plotNicheClusterConnectivity
+- title: Auxiliary
+  desc: Auxiliary functions.
+- contents:
+  - callSpdep
 - title: AI technologies
   desc:
 - contents: