% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plot_mov.cor.R
\name{plot.mov_cor_dm}
\alias{plot.mov_cor_dm}
\title{Plot method for moving dendrometer-climate correlation}
\usage{
\method{plot}{mov_cor_dm}(
  x,
  y = NULL,
  sig.only = TRUE,
  ci = 0.95,
  clim_vars = "all",
  type = c("heatmap", "line", "facet", "peak", "compare"),
  x_axis = c("time", "doy"),
  use_adjusted = TRUE,
  show_na = TRUE,
  show_ci = FALSE,
  sig_mode = c("outline", "point", "filter", "none"),
  annotate_peak = FALSE,
  show_window_label = TRUE,
  compare_with = NULL,
  compare_labels = NULL,
  low_col = "red",
  mid_col = "white",
  high_col = "blue",
  na_col = "grey79",
  line_size = 0.5,
  point_size = 1.8,
  alpha_sig = 0.9,
  ...
)
}
\arguments{
\item{x}{Object returned by \code{mov.cor.dm()}.}

\item{y}{Unused.}

\item{sig.only}{Logical. If \code{TRUE}, only significant windows are shown in
heatmaps and significance is highlighted in other plot types.}

\item{ci}{Numeric confidence level between 0 and 1. For non-bootstrap
results, significance is based on \code{p_val < 1 - ci} or
\code{p_adj < 1 - ci}. For bootstrap results, the stored logical
\code{significance} column is used.}

\item{clim_vars}{Character vector of climate variables to plot, or
\code{"all"} for all variables.}

\item{type}{Plot type. One of \code{"heatmap"}, \code{"line"},
\code{"facet"}, \code{"peak"}, or \code{"compare"}.}

\item{x_axis}{X-axis style. One of \code{"time"} or \code{"doy"}.}

\item{use_adjusted}{Logical. For non-bootstrap objects, if \code{TRUE},
significance uses \code{p_adj}; otherwise \code{p_val}.}

\item{show_na}{Logical. If \code{TRUE}, missing values are shown in heatmaps.}

\item{show_ci}{Logical. If \code{TRUE}, bootstrap confidence intervals are
shown in line/facet/compare plots when available.}

\item{sig_mode}{One of \code{"outline"}, \code{"point"}, \code{"filter"},
or \code{"none"} describing how significance is displayed in non-heatmap plots.}

\item{annotate_peak}{Logical. If \code{TRUE}, the strongest absolute
correlation is marked for each climate variable in line/facet/compare plots.}

\item{show_window_label}{Logical. If \code{TRUE}, \code{type = "peak"} adds
the climate transformation settings above each bar.}

\item{compare_with}{Optional list of additional \code{mov_cor_dm} objects for
comparison. Used only when \code{type = "compare"}.}

\item{compare_labels}{Optional character vector of labels for the comparison
objects. If \code{NULL}, defaults are generated automatically.}

\item{low_col}{Colour for negative correlations.}

\item{mid_col}{Colour for zero correlations.}

\item{high_col}{Colour for positive correlations.}

\item{na_col}{Fill colour for missing values in heatmaps.}

\item{line_size}{Numeric line width for line plots.}

\item{point_size}{Numeric point size for significance markers and peak markers.}

\item{alpha_sig}{Numeric transparency used for significance highlighting.}

\item{...}{Unused.}
}
\value{
A \code{ggplot2} object, returned invisibly.
}
\description{
S3 plotting method for output of \code{mov.cor.dm()}.
Supports heatmaps, line plots, faceted line plots, peak-correlation summaries,
and comparison across multiple \code{mov.cor.dm()} objects.
}
