Overview

This notebook assembles the WGCNA module perturbation figure (Figure 6) from pre-generated panel RDS files.

Panels: - A: CTRL consensus network dendrogram with module colors - B: Delta kWithin boxplot (connectivity change per module) with GO annotations - C: Hub gene connectivity scatter plot (CTRL vs Inv4m)

Setup

suppressPackageStartupMessages({
  library(tidyverse)
  library(here)
  library(cowplot)
  library(patchwork)
})

# Load project paths
source(here("scripts", "utils", "setup_paths.R"))
paths <- setup_project_paths("inversion_paper")

# Pipeline run directory
run_dir <- here("results/inversion_paper/field_perturbation/run_20251231_201332")

# Panel paths
panel_paths <- list(
  A = file.path(run_dir, "04_consensus_networks/ctrl/dendrogram_plot.rds"),
  B = file.path(run_dir, "06_preservation/delta_kWithin_boxplot_annotated.rds"),
  C = file.path(run_dir, "07_module_annotation/hub_connectivity_plot.rds")
)

# Verify all panels exist
for (panel in names(panel_paths)) {
  if (!file.exists(panel_paths[[panel]])) {
    stop(paste("Panel", panel, "not found:", panel_paths[[panel]]))
  }
}
cat("All panel files found.\n")

## All panel files found.

Load Panels

p_A <- readRDS(panel_paths$A)
p_B <- readRDS(panel_paths$B)
p_C <- readRDS(panel_paths$C)

cat("Panels loaded successfully.\n")

## Panels loaded successfully.

Preview Individual Panels

Panel A: Consensus Network Dendrogram

print(p_A)

Panel B: Delta kWithin Boxplot

print(p_B)

Panel C: Hub Gene Connectivity

print(p_C)

Alternative Layouts

Layout: A on top, B and C side by side below

# Bottom row: B and C side by side
bottom_row <- plot_grid(
  p_B,
  p_C,
  ncol = 2,
  labels = c("B", "C"),
  label_size = 35,
  rel_widths = c(1, 1)
)

# Combined: A on top, B+C below
fig_combined <- plot_grid(
  p_A,
  bottom_row,
  ncol = 1,
  labels = c("A", ""),
  label_size = 35,
  rel_heights = c(0.3, 0.7)
)

ggsave(
  file.path(paths$figures, "WGCNA_module_perturbation.png"),
  fig_combined,
  width = 14, height = 12,
  dpi = 300
)

ggsave(
  file.path(paths$figures, "WGCNA_module_perturbation.pdf"),
  fig_combined,
  width = 14, height = 12
)

print(fig_combined)

Session Info

sessionInfo()

## R version 4.5.2 (2025-10-31)
## Platform: aarch64-apple-darwin20
## Running under: macOS Tahoe 26.2
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C.UTF-8/C.UTF-8/C.UTF-8/C/C.UTF-8/C.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] patchwork_1.3.2 cowplot_1.2.0   here_1.0.2      lubridate_1.9.4
##  [5] forcats_1.0.1   stringr_1.6.0   dplyr_1.1.4     purrr_1.2.0    
##  [9] readr_2.1.6     tidyr_1.3.2     tibble_3.3.0    ggplot2_4.0.1  
## [13] tidyverse_2.0.0
## 
## loaded via a namespace (and not attached):
##  [1] yulab.utils_0.2.3  rappdirs_0.3.3     sass_0.4.10        generics_0.1.4    
##  [5] ggplotify_0.1.3    stringi_1.8.7      hms_1.1.4          digest_0.6.39     
##  [9] magrittr_2.0.4     evaluate_1.0.5     grid_4.5.2         timechange_0.3.0  
## [13] RColorBrewer_1.1-3 fastmap_1.2.0      rprojroot_2.1.1    jsonlite_2.0.0    
## [17] ggrepel_0.9.6      scales_1.4.0       textshaping_1.0.4  jquerylib_0.1.4   
## [21] cli_3.6.5          rlang_1.1.6        withr_3.0.2        cachem_1.1.0      
## [25] yaml_2.3.12        otel_0.2.0         tools_4.5.2        tzdb_0.5.0        
## [29] vctrs_0.6.5        R6_2.6.1           gridGraphics_0.5-1 lifecycle_1.0.4   
## [33] fs_1.6.6           ragg_1.5.0         pkgconfig_2.0.3    pillar_1.11.1     
## [37] bslib_0.9.0        gtable_0.3.6       Rcpp_1.1.0         glue_1.8.0        
## [41] systemfonts_1.3.1  xfun_0.55          tidyselect_1.2.1   knitr_1.51        
## [45] dichromat_2.0-0.1  farver_2.1.2       htmltools_0.5.9    labeling_0.4.3    
## [49] rmarkdown_2.30     compiler_4.5.2     S7_0.2.1

WGCNA Module Perturbation Figure Assembly

Analysis Pipeline

2026-02-16