% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot-ml-heatmap.R
\name{plot_ml_heatmap}
\alias{plot_ml_heatmap}
\title{Multilayer Network Heatmap}
\usage{
plot_ml_heatmap(
  x,
  layer_list = NULL,
  colors = "viridis",
  layer_spacing = 2.5,
  skew = 0.4,
  compress = 0.6,
  show_connections = FALSE,
  connection_color = "#E63946",
  connection_style = "dashed",
  show_borders = TRUE,
  border_color = "black",
  border_width = 1,
  cell_border_color = "white",
  cell_border_width = 0.2,
  show_labels = TRUE,
  label_size = 5,
  show_legend = TRUE,
  legend_title = "Weight",
  title = NULL,
  limits = NULL,
  na_color = "grey90",
  threshold = 0
)
}
\arguments{
\item{x}{A list of matrices (one per layer), a group_tna object,
cograph_network, or a single matrix with layer_list specified.}

\item{layer_list}{Optional list defining layers, column name string,
or NULL for auto-detection from cograph_network nodes.}

\item{colors}{Color palette: "viridis", "heat", "blues", "reds", "inferno",
"plasma", or a vector of colors. Default "viridis".}

\item{layer_spacing}{Vertical spacing between layers. Default 2.5.}

\item{skew}{Horizontal skew for perspective effect (0-1). Default 0.4.}

\item{compress}{Vertical compression for perspective (0-1). Default 0.6.}

\item{show_connections}{Show inter-layer connection lines? Default FALSE.}

\item{connection_color}{Color for inter-layer connections. Default "#E63946".}

\item{connection_style}{Line style: "dashed", "solid", "dotted". Default "dashed".}

\item{show_borders}{Show layer outline borders? Default TRUE.}

\item{border_color}{Color for layer borders. Default "black".}

\item{border_width}{Width of layer borders. Default 1.}

\item{cell_border_color}{Color for cell borders. Default "white".}

\item{cell_border_width}{Width of cell borders. Default 0.2.}

\item{show_labels}{Show layer name labels? Default TRUE.}

\item{label_size}{Size of layer labels. Default 5.}

\item{show_legend}{Show color legend? Default TRUE.}

\item{legend_title}{Title for legend. Default "Weight".}

\item{title}{Plot title. Default NULL.}

\item{limits}{Color scale limits c(min, max). NULL for auto.}

\item{na_color}{Color for NA values. Default "grey90".}

\item{threshold}{Minimum absolute value to display. Cells with
\code{abs(value) < threshold} are set to NA (rendered as background).
Default 0.}
}
\value{
A ggplot2 object.
}
\description{
Visualizes multiple network layers as heatmaps on tilted 3D-perspective planes,
similar to the plot_mlna network visualization style.
}
\examples{
set.seed(1)
layers <- list(
  L1 = matrix(runif(16), 4, 4),
  L2 = matrix(runif(16), 4, 4),
  L3 = matrix(runif(16), 4, 4))
plot_ml_heatmap(layers)
plot_ml_heatmap(layers, show_connections = TRUE, colors = "plasma")

}
