plot_diff_network: Plot Differential Gene Regulatory Network (Combined/Separate...

In scNPM: Single-Cell Network Propensity Matching

Plot Differential Gene Regulatory Network (Combined/Separate Mode)

Description

Plots differential networks (treatment - control) with flexible output: - Combined mode: solid/dashed edges in a single plot (default) - Separate mode: solid/dashed edges as two independent plots

Usage

plot_diff_network(
  diff_mat,
  gene_names,
  solid_threshold = 0.5,
  dashed_threshold = -0.5,
  solid_color = "#ADD8E6",
  dashed_color = "#ADD8E6",
  output_mode = c("combined", "separate"),
  ...
)

Arguments

diff_mat	Differential matrix (treatment - control, rows/columns = gene names). Matrices returned by Bayesian-mode run_scNPM carry a scNPM_selection attribute; its selected edge masks are used directly, without re-thresholding.
gene_names	Vector of gene names (matches diff_mat row/column names).
solid_threshold	Minimum positive difference for unannotated matrices (default = 0.5); ignored for matrices carrying Bayesian selection masks.
dashed_threshold	Maximum negative difference for unannotated matrices (default = -0.5); ignored for matrices carrying Bayesian selection masks.
solid_color	Color for solid edges (treatment-enhanced, default = "#ADD8E6", the original scNPM light blue; set e.g. "#2ECC71" for green).
dashed_color	Color for dashed edges (treatment-reduced, default = "#ADD8E6", the original scNPM light blue; set e.g. "#F39C12" for orange).
output_mode	Output type: "combined" (single plot, default) or "separate" (two plots).
...	Additional parameters passed to plot_network_core() (separate mode) or internal plotting (combined mode).

Value

- If output_mode = "combined": ggplot object (single plot with solid/dashed edges) or NULL (no edges) - If output_mode = "separate": list of ggplot objects (solid/dashed) or NULL for empty edges

Examples

# Self-contained example with a small random differential matrix (< 5 sec)
set.seed(1)
gn <- paste0("Gene_", 1:10)
dm <- matrix(rnorm(100), 10, 10, dimnames = list(gn, gn))
dm <- (dm + t(dm)) / 2
diag(dm) <- 0

# Mode 1 - Combined (solid+dashed in one plot, default colors: light blue)
p_combined <- plot_diff_network(
  diff_mat = dm,
  gene_names = gn,
  output_mode = "combined"
)

# Mode 2 - Separate (solid/dashed as two plots; custom colors optional)
p_separate <- plot_diff_network(
  diff_mat = dm,
  gene_names = gn,
  output_mode = "separate",
  solid_color = "#2ECC71",
  dashed_color = "#F39C12",
  label_size = 3
)

scNPM documentation built on Oct. 19, 2026, 5:10 p.m.