Workflow overview | Demonstration data | The linkage_summary class | Counting linkages across groups | Total counts | Grouped counts | Testing differential linkages | Two-group comparisons | Multi-group comparisons | Visualizing differential linkages | Example run | Related Articles

Installation | Options and Setup | Data preparation | Loading TF and receptor-ligand data | Loading SCENIC results | Loading the CellPhoneDB database | Optional: Adding interactions manually | Analysis with domino objects | Required inputs from data set | Create domino object | Build the domino network | Visualization of domino results | Summarize TF activity and linkages | Cumulative signaling between clusters | Specific Signaling Interactions between Clusters | Example run | Related articles

Object contents | Access functions | Input data | Calculations | Linkages | Signaling Matrices | Build information | Related articles

Setup and data load | Heatmaps | Correlations between receptors and transcription factors | Heatmap of Transcription Factor Activation Scores | Heatmap of incoming signaling for a cluster | Heatmap of signaling between clusters | Network plots | Network showing L-R-TF signaling between clusters | Network showing interaction strength across data | Other types of plots | Chord diagrams connecting ligands and receptors | Scatter plot to visualize correlation | Related articles

Importing Local Libraries | Preparing the Data | Creating a Basic ScatterHatch Plot | Customizing ScatterHatch Plot | Changing the Order of Pattern Assignment | Changing the Angles of each Pattern | scatterHatch() Arguments Explained | Pattern Aesthetics Arguments | Session Info