collection of funtions used in network analysis Compute pairwise cell correlations and return edge list

Usage

traces_correlation(
  method = "combined",
  traces,
  network_dir,
  filename,
  interval_name = "Full",
  grid_coord,
  cell_nodes,
  plot_matrix = TRUE,
  filter_nonrhythmic = FALSE
)

Arguments

method: Character; correlation method, either "spearman" or "combined" (Spearman + FFT-based rhythm similarity). Defaults to "combined".
traces: Numeric matrix of cell fluorescence traces (cells × frames).
network_dir: Character; directory for saving correlation matrix plots.
filename: Character; file identifier used in plot filenames.
interval_name: Character; interval label used in plot filenames. Defaults to "Full".
grid_coord: Data frame of grid coordinates with columns X and Y, used for spatial weighting in "combined" mode.
cell_nodes: Data frame of node metadata; must contain a name column matching row indices of traces.
plot_matrix: Logical; whether to save a heatmap of the correlation matrix. Defaults to TRUE.
filter_nonrhythmic: Logical; whether to remove edges with NA weights before returning. Defaults to FALSE.

Value

A data frame of edges with columns from, to, and weight (Fisher z-transformed correlation).