One-shot, non-interactive RMT threshold scan with auto selection

Usage

ggNetView_RMT(
  mat,
  transfrom.method = c("none", "scale", "center", "log2", "log10", "ln", "rrarefy",
    "rrarefy_relative"),
  method = c("WGCNA", "SpiecEasi", "SPARCC", "cor"),
  cor.method = c("pearson", "kendall", "spearman"),
  SpiecEasi.method = c("mb", "glasso"),
  nr_thresholds = 51,
  interval = NULL,
  unfold.method = c("gaussian", "spline"),
  bandwidth = "nrd0",
  nr.fit.points = 51,
  discard.outliers = TRUE,
  discard.zeros = TRUE,
  min.mat.dim = 40,
  max.ev.spacing = 3,
  save_plots = FALSE,
  out_dir = "RMT_plots",
  verbose = TRUE,
  seed = 1115
)

Arguments

mat: Numeric matrix. A numeric matrix with samples in colums and variables in rows #' @param transfrom.method Character. Data transformation methods applied before correlation analysis. Options include: "none" (raw data), "scale" (z-score standardization), "center" (mean centering only), "log2" (log2 transfrom), "log10" (log10 transfrom), "ln" (natural transfrom ), "rrarefy" (random rarefaction using vegan::rrarefy), "rrarefy_relative" (rarefy then convert to relative abundance).
method: Character. Relationship analysis methods. Options include: "WGCNA", "SpiecEasi", "SPARCC" and "cor".
cor.method: Character. Correlation analysis method. Options include "pearson", "kendall", and "spearman".
SpiecEasi.method: Character. Method used in SpiecEasi network inference; options include "mb" and "glasso".
nr_thresholds: Integer. Number of thresholds to scan (default 51).
interval: Optional numeric length-2 vector [min, max] for scanning range over |mat| upper triangle (default auto).
unfold.method: "gaussian" or "spline" (default "gaussian").
bandwidth: Bandwidth for gaussian unfolding (passed to stats::density), default "nrd0".
nr.fit.points: Integer, number of support points for spline unfolding (default 51).
discard.outliers: Logical. Remove eigenvalue outliers via IQR before unfolding (default TRUE).
discard.zeros: Logical. Drop all-zero rows/cols after thresholding (default TRUE).
min.mat.dim: Integer. Early stop if effective dim < this (default 40).
max.ev.spacing: Numeric. Cutoff for spacing tail when computing NNSD metrics (default 3).
save_plots: Logical. Save PNGs (non-interactive) into out_dir (default FALSE).
out_dir: Character. Output directory for plots (default "RMT_plots").
verbose: Logical. Print progress (default TRUE).
seed: Integer (default = 1115). Random seed for reproducibility.

Value

A list with: chosen_threshold, chosen_reason, tested_thresholds, scores (data.frame), unfolded (last-step unfolding), meta (matrix info & params), plots (file paths if saved).

Examples

NULL
#> NULL


# m <- cor(scale(matrix(rnorm(40000), 200, 200)))
# res <- ggNetView_RMT(m, save_plots=TRUE)
# res$chosen_threshold