% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/motifs-extract.R
\name{plot.cograph_motif_analysis}
\alias{plot.cograph_motif_analysis}
\title{Plot Motif Analysis Results}
\usage{
\method{plot}{cograph_motif_analysis}(
  x,
  type = c("triads", "types", "significance", "patterns"),
  n = 20,
  colors = c("#2166AC", "#B2182B"),
  res = 72,
  node_size = 5,
  label_size = 7,
  title_size = 7,
  stats_size = 5,
  ncol = 5,
  legend = TRUE,
  color = "#800020",
  spacing = 1,
  ...
)
}
\arguments{
\item{x}{A \code{cograph_motif_analysis} object from \code{\link[=extract_motifs]{extract_motifs()}}}

\item{type}{Plot type: "triads" (default network diagrams), "types" (bar plot),
"significance" (z-score plot), or "patterns" (abstract MAN patterns)}

\item{n}{Number of triads to show. Default 20.}

\item{colors}{Colors for visualization. Default blue/red.}

\item{res}{Resolution for scaling (not used with grid graphics). Default 72.}

\item{node_size}{Size of nodes (1-10 scale, like splot). Default 5.}

\item{label_size}{Font size for node labels (3-letter abbreviations). Default 7.}

\item{title_size}{Font size for motif type title (e.g., "120C"). Default 7.}

\item{stats_size}{Font size for statistics text (n, z, p). Default 5.}

\item{ncol}{Number of columns in the plot grid. Default 5.}

\item{legend}{Logical, show abbreviation legend at bottom? Default TRUE.}

\item{color}{Color for nodes, edges, and labels. Default "#800020" (maroon).}

\item{spacing}{Spacing multiplier between cells (0.5-2). Default 1.}

\item{...}{Additional arguments (unused)}
}
\value{
Invisibly returns NULL for triad plots, or a ggplot2 object for other types.
}
\description{
Create visualizations for motif analysis results including network diagrams
of triads, bar plots of type distributions, and significance plots.
}
\examples{
\dontrun{
Mod <- tna::tna(tna::group_regulation)
m <- extract_motifs(Mod, significance = TRUE)

# Default network diagram
plot(m)

# Customize appearance
plot(m, node_size = 0.15, label_size = 6, title_size = 9)

# Change layout
plot(m, ncol = 4, n = 12)

# Other plot types
plot(m, type = "types")
plot(m, type = "significance")
}

}
\seealso{
\code{\link[=extract_motifs]{extract_motifs()}} for the analysis that produces this object,
\code{\link[=motif_census]{motif_census()}} for statistical motif analysis

Other motifs: 
\code{\link{extract_motifs}()},
\code{\link{extract_triads}()},
\code{\link{get_edge_list}()},
\code{\link{motif_census}()},
\code{\link{motifs}()},
\code{\link{plot.cograph_motifs}()},
\code{\link{subgraphs}()},
\code{\link{triad_census}()}
}
\concept{motifs}
