% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/CellWindX_MarkerHeatmap.R
\name{CellWindX_MarkerHeatmap}
\alias{CellWindX_MarkerHeatmap}
\title{Draw marker-gene heatmap across annotated cell groups}
\usage{
CellWindX_MarkerHeatmap(
  marker_result,
  value_col = c("avg_expr", "pct_expr", "avg_expr_positive"),
  scale_method = c("zscore", "none"),
  plot_engine = c("complex", "ggplot"),
  palette = c("shanshui", "chongqing_modern", "girlish"),
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  show_row_names = TRUE,
  show_column_names = TRUE,
  column_names_rot = 45,
  round_cell = TRUE,
  cell_width_mm = 5.5,
  cell_height_mm = 5.5,
  row_fontsize = 10,
  column_fontsize = 9,
  legend_position = "right",
  heatmap_title = NULL,
  zscore_clip = 2,
  output_file = NULL,
  output_width = 9,
  output_height = 5,
  dpi = 300,
  draw = TRUE
)
}
\arguments{
\item{marker_result}{A result object returned by \code{CellWindX_TopMarkersStats()},
or a data frame containing marker expression statistics.}

\item{value_col}{Character string. Value column used for heatmap visualization.
One of \code{"avg_expr"}, \code{"pct_expr"}, or \code{"avg_expr_positive"}.}

\item{scale_method}{Character string. Scaling method. One of \code{"zscore"} or \code{"none"}.}

\item{plot_engine}{Character string. Plotting engine. One of \code{"complex"} or \code{"ggplot"}.}

\item{palette}{Character string. Built-in CellWindX palette.}

\item{cluster_rows}{Logical. Whether to cluster rows.}

\item{cluster_columns}{Logical. Whether to cluster columns.}

\item{show_row_names}{Logical. Whether to show row names.}

\item{show_column_names}{Logical. Whether to show column names.}

\item{column_names_rot}{Numeric. Rotation angle of column names.}

\item{round_cell}{Logical. Whether to draw rounded cells when using ComplexHeatmap.}

\item{cell_width_mm}{Numeric. Cell width in millimeters.}

\item{cell_height_mm}{Numeric. Cell height in millimeters.}

\item{row_fontsize}{Numeric. Row name font size.}

\item{column_fontsize}{Numeric. Column name font size.}

\item{legend_position}{Character string. Legend position.}

\item{heatmap_title}{Character string or NULL. Heatmap title.}

\item{zscore_clip}{Numeric. Z-score clipping threshold.}

\item{output_file}{Character string or NULL. Optional output file path.}

\item{output_width}{Numeric. Output width in inches.}

\item{output_height}{Numeric. Output height in inches.}

\item{dpi}{Numeric. Output resolution.}

\item{draw}{Logical. Whether to draw the heatmap immediately when using ComplexHeatmap.}
}
\value{
A list with class \code{"CellWindX_MarkerHeatmap"}.
}
\description{
\code{CellWindX_MarkerHeatmap()} visualizes marker gene expression statistics
across annotated cell groups using either \code{ComplexHeatmap} or \code{ggplot2}.
}
