% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/vis-gsea-core.R
\name{.gsea_nb_core}
\alias{.gsea_nb_core}
\title{Internal GSEA Native Plotting Engine}
\usage{
.gsea_nb_core(
  object,
  geneSetID,
  subPlot = 3,
  curveCol = c("#76BA99", "#EB4747", "#996699"),
  htCol = c("#08519C", "#A50F15"),
  lineSize = 0.8,
  addPval = FALSE,
  pvalX = 0.9,
  pvalY = 0.9,
  pvalSize = 4,
  pCol = "grey0",
  nesDigit = 2,
  pDigit = 2,
  show_contrast_in_axis = FALSE,
  left_group = "Left",
  right_group = "Right",
  base_size = 14,
  subRatio = c(0.5, 0.2, 0.3),
  rankSeq = 5000,
  htHeight = 0.3,
  htAlpha = 0.8
)
}
\arguments{
\item{object}{gseaResult object.}

\item{geneSetID}{Character vector of pathway IDs.}

\item{subPlot}{Integer, 1/2/3.}

\item{curveCol}{Curve color vector.}

\item{htCol}{Heatmap gradient colors.}

\item{lineSize}{Line width for enrichment curve.}

\item{addPval}{Logical, add NES/Pvalue text annotation (single pathway only).}

\item{pvalX}{X position for pval text (relative fraction).}

\item{pvalY}{Y position for pval text (relative fraction).}

\item{pvalSize}{Text size for pval annotation.}

\item{pCol}{Color for pval text.}

\item{nesDigit}{NES rounding digits.}

\item{pDigit}{P-value rounding digits.}

\item{show_contrast_in_axis}{Logical, if TRUE shows "Left vs Right" on X-axis.}

\item{left_group}{Left group label.}

\item{right_group}{Right group label.}

\item{base_size}{Theme base size.}

\item{subRatio}{Relative heights for 3 panels.}

\item{rankSeq}{X-axis break interval for rank plot.}

\item{htHeight}{Relative height of heatmap strip inside Panel 2.}

\item{htAlpha}{Alpha for heatmap rectangles.}
}
\value{
Named list: p1 (curve), p2 (heatmap strip), p3 (rank distribution),
  data_ga, gsdata, glist.
}
\description{
Core plotting logic migrated from GseaVis::gseaNb,
  stripped of unused features (newGsea, filePath, KEGG, geneExpHt, etc.).
  Returns a list of ggplot objects for downstream assembly via patchwork.
}
\keyword{internal}
