Visualization Gallery

Introduction

MultiNicheNet provides a comprehensive suite of visualization functions for exploring and communicating cell-cell communication analysis results. This gallery showcases all major plot types with example code.

Overview of Visualization Functions

Function	Description	Use Case
`make_sample_lr_prod_plots`	L-R product across samples	Sample-level patterns
`make_ligand_receptor_lfc_plot`	Log fold change visualization	DE comparison
`make_circos_lr`	Circos plot of interactions	Network overview
`make_mushroom_plot`	Mushroom-style bubble plot	Multi-criteria display
`make_ligand_activity_plots`	Ligand activity heatmaps	Activity inference
`make_target_gene_plots`	Target gene expression	Downstream effects

Sample-Level Visualizations

Ligand-Receptor Product Plots

The L-R product plot shows the combined expression of ligand-receptor pairs across samples:

library(multinichenetr)
library(dplyr)

# Load example output (from your analysis)
# output <- multi_nichenet_analysis(...)

# Select top interactions
prioritized_tbl <- output$prioritization_tables$group_prioritization_tbl %>%
  filter(fraction_expressing_ligand_receptor > 0) %>%
  filter(group == "High") %>%
  top_n(15, prioritization_score)

# Create L-R product plot
p_lr_prod <- make_sample_lr_prod_plots(
  output$prioritization_tables,
  prioritized_tbl
)
print(p_lr_prod)

Differential Expression Visualization

# Log fold change plot for ligands and receptors
p_lfc <- make_ligand_receptor_lfc_plot(
  receiver_de = output$ligand_activities_targets_DEgenes$receiver_de,
  prioritized_tbl = prioritized_tbl,
  contrast_oi = "High-Low"
)
print(p_lfc)

Network Visualizations

Circos Plots

Circos plots provide a global view of cell-cell communication patterns:

# Create circos plot
make_circos_lr(
  prioritized_tbl = prioritized_tbl,
  colors_sender = c("Macrophage" = "#E41A1C", "Fibroblast" = "#377EB8"),
  colors_receiver = c("Tcell" = "#4DAF4A", "Bcell" = "#984EA3")
)

Chord Diagrams

For a more detailed view with ligand-receptor annotations:

Multi-Criteria Bubble Plots

Mushroom Plots

The mushroom plot is a signature visualization of MultiNicheNet, displaying multiple criteria simultaneously:

# Create mushroom plot
p_mushroom <- make_mushroom_plot(
  prioritization_tables = output$prioritization_tables,
  top_n = 20,
  contrast_oi = "High-Low"
)
print(p_mushroom)

Ligand Activity Visualizations

Activity Heatmaps

# Ligand activity heatmap
p_activity <- make_ligand_activity_plots(
  ligand_activities_targets_DEgenes = output$ligand_activities_targets_DEgenes,
  receiver_oi = "Tcell",
  top_n_ligands = 20
)
print(p_activity)

Target Gene Visualizations

Target Gene Expression

# Target gene expression plot
p_targets <- make_target_gene_plots(
  ligand_activities_targets_DEgenes = output$ligand_activities_targets_DEgenes,
  ligand_oi = "TGFB1",
  receiver_oi = "Tcell"
)
print(p_targets)

Summary Statistics

Overview Barplots

Customization Tips

Color Palettes

Export High-Quality Figures

# Save publication-quality figures
ggsave(
  "figure_1.pdf",
  plot = p_mushroom,
  width = 12,
  height = 8,
  dpi = 300
)

# For presentations
ggsave(
  "figure_1.png",
  plot = p_mushroom,
  width = 12,
  height = 8,
  dpi = 150,
  bg = "white"
)

Session Information

sessionInfo()

Maintained by Zaoqu Liu