% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/gedi_plots.R
\name{.plot_embedding_base}
\alias{.plot_embedding_base}
\title{Plot 2D Embedding (Base Function)}
\usage{
.plot_embedding_base(
  embedding,
  color = NULL,
  color_limits = NULL,
  palette = c("blue", "lightgrey", "red"),
  randomize = TRUE,
  point_size = 0.3,
  alpha = 0.9,
  raster = FALSE,
  xlab = "Dim 1",
  ylab = "Dim 2",
  title = NULL,
  legend_title = NULL
)
}
\arguments{
\item{embedding}{Matrix (N x 2) with x and y coordinates for each cell}

\item{color}{Vector of length N for coloring points, or NULL for uniform color}

\item{color_limits}{Numeric vector c(low, high) for color scale limits,
or NULL to auto-compute from data (uses 99th percentile for symmetric limits)}

\item{palette}{Character vector of colors for continuous scale (length 3 for diverging)}

\item{randomize}{Logical, whether to randomize point order before plotting}

\item{point_size}{Numeric, size of points}

\item{alpha}{Numeric, transparency of points (0-1)}

\item{raster}{Logical, use rasterization for large datasets (>100k points)}

\item{xlab}{Character, x-axis label}

\item{ylab}{Character, y-axis label}

\item{title}{Character, plot title}

\item{legend_title}{Character, legend title (auto-detected if NULL)}
}
\value{
ggplot2 object
}
\description{
Base function for plotting 2D embeddings with customizable coloring.
Supports both continuous and discrete color variables.
}
\keyword{internal}
