# Spatially Aware Cell-Cell Interaction Analysis

## Documentation for package ‘SpaCCI’ version 1.0.3

- DESCRIPTION file.

## Help Pages

Find_regional_IDs | Find the spatial neighborhood Spot IDs
GetShuffledCT | Perform a Deranged Shuffle of Cell Types
Global_Permutations | Perform Global Permutations
Local_Regional_Permutations | Perform Local and Regional Permutations
LR_database | Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
plot_localized | Plot Localized Hotspot Pattern
plot_localized_Seurat | Plot Localized Hotspot Pattern on Seurat Object
plot_SpaCCI_chordDiagram | Plot SpaCCI Results on Chord Diagram
plot_SpaCCI_heatmap | Plot SpaCCI Results on the heatmap Visualize inferred significant cell-cell interactions using a heatmap
plot_SpaCCI_local | Plot SpaCCI Localized Interaction Results
plot_SpaCCI_local_Strength | Plot SpaCCI Localized Interaction Strength Results
plot_Strength_localized | Plot Localized Hotspot Strength Pattern
plot_Strength_Seurat | Plot Localized Hotspot Strength Pattern on Seurat Object
possible_L_R_pairs_cellchat | CellChat Database: Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_Cellinker | Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_cellphoneDB | Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_connectome | Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
possible_L_R_pairs_ICELLNET | Identify Possible Ligand-Receptor Pairs for Cell-Cell Communication
random_region | Select Closest Spatial IDs to a Center Point: this is used for permutation
result_global | result_global data for SpaCCI
result_local | result_local data and spatial coordinates for SpaCCI Local Regional Data
result_local_spatial_coords_df | Local Spatial Coordinates Data Frame
result_regional | result_regional data for SpaCCI
run_SpaCCI | Run SpaCCI Analysis
scPalette | Generate a Color Palette
SpaCCI_global | Infer Cell-Cell Interactions on a Global Scale
SpaCCI_local | Infer Cell-Cell Interactions on a Local Scale
SpaCCI_region | Infer Cell-Cell Interactions in a Specified Region
test_data | Test data for SpaCCI