Package index • dominoSignal

Domino Classes

An object class designed to store information used and produced in dominoSignal analysis

domino-class domino: The domino class

linkage_summary-class linkage_summary: The domino linkage summary class

Analysis Functions

Functions for performing cell-cell communication analysis with the dominoSignal package

create_rl_map_cellphonedb(): Create a receptor - ligand map from a CellPhoneDB signaling database

create_regulon_list_scenic(): Create a list of genes in regulons inferred by SCENIC

create_domino(): Create a domino object and prepare it for network construction

build_domino(): Calculate a signaling network for a domino object

summarize_linkages(): Summarize linkages from multiple domino objects

test_differential_linkages(): Statistical test for differential linkages across multiple domino results

Plotting Functions

Functions for visualizing dominoSignal analysis results

Heatmaps

cor_heatmap(): Create a heatmap of correlation between receptors and transcription factors

feat_heatmap(): Create a heatmap of features organized by cluster

incoming_signaling_heatmap(): Create a cluster incoming signaling heatmap

signaling_heatmap(): Create a network heatmap

Network Plots

gene_network(): Create a gene association network

signaling_network(): Create a cluster to cluster signaling network diagram

Other Plots

circos_ligand_receptor(): Plot expression of a receptor's ligands by other cell types as a chord plot

cor_scatter(): Create a correlation plot between TF and receptor

plot_differential_linkages(): Plot differential linkages among domino results ranked by a comparative statistic

Helper Functions

Convenience functions for working with dominoSignal objects

Access functions

dom_clusters(): Access clusters

dom_correlations(): Access correlations

dom_counts(): Access counts

dom_database(): Access database

dom_de(): Access differential expression

dom_info(): Access build information

dom_linkages(): Access linkages

dom_network_items(): Access all features, receptors, or ligands present in a signaling network.

dom_signaling(): Access signaling

dom_tf_activation(): Access transcription factor activation

dom_zscores(): Access z-scores

Misc. utility functions

add_rl_column(): Adds a column to the RL signaling data frame.

count_linkage(): Count occurrences of linkages across multiple domino results from a linkage summary

mean_ligand_expression(): Calculate mean ligand expression as a data frame for plotting in circos plot

print(<domino>): Print domino object

rename_clusters(): Renames clusters in a domino object

show(<domino>): Show domino object information

Example Data

Example data used for testing and demonstration purposes

CellPhoneDB: CellPhoneDB subset

SCENIC: SCENIC AUC subset

PBMC: PBMC RNAseq data subset

mock_linkage_summary(): Create a mock linkage summary object