enrichCluster.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/3.enrichCluster.R
\name{enrichCluster}
\alias{enrichCluster}
\title{Perform GO/KEGG Enrichment Analysis for Multiple Clusters}
\usage{
enrichCluster(
  object = NULL,
  type = c("BP", "MF", "CC", "KEGG", "ownSet"),
  TERM2GENE = NULL,
  TERM2NAME = NULL,
  OrgDb = NULL,
  id.trans = TRUE,
  fromType = "SYMBOL",
  toType = c("ENTREZID"),
  readable = TRUE,
  organism = "hsa",
  pvalueCutoff = 0.05,
  topn = 5,
  seed = 5201314,
  add.gene = FALSE,
  use_internal_data = FALSE,
  heatmap.type = c("plot_pseudotime_heatmap2", "plot_genes_branched_heatmap2",
    "plot_multiple_branches_heatmap2"),
  ...
)
}
\arguments{
\item{object}{An object containing clustering results.
This is clusterData object. Alternatively, it can be a \code{CellDataSet} object, in which case the function can also visualize pseudotime data.}

\item{type}{Character. The type of enrichment analysis to perform. Options include:
\itemize{
\item \code{"BP"}: Biological Process (GO)
\item \code{"MF"}: Molecular Function (GO)
\item \code{"CC"}: Cellular Component (GO)
\item \code{"KEGG"}: KEGG Pathway analysis
\item \code{"ownSet"}: Custom gene set enrichment, requiring \code{TERM2GENE} and optionally \code{TERM2NAME}.
}}

\item{TERM2GENE}{A data frame containing mappings of terms to genes. Required when \code{type = "ownSet"}.
This must be a two-column data frame, where the first column is the term and the second column is the gene.}

\item{TERM2NAME}{A data frame containing term-to-name mappings. Optional when \code{type = "ownSet"}.
This must also be a two-column data frame, where the first column is the term and the second column is the name.}

\item{OrgDb}{An organism database object (e.g., \code{org.Hs.eg.db} for human or \code{org.Mm.eg.db} for mouse),
used for GO or KEGG enrichment analysis.}

\item{id.trans}{Logical. Whether to perform gene ID transformation. Default is \code{TRUE}.}

\item{fromType}{Character. The type of the input gene IDs (e.g., \code{"SYMBOL"}, \code{"ENSEMBL"}). Default is \code{"SYMBOL"}.}

\item{toType}{Character. The target ID type for transformation using \code{clusterProfiler::bitr}
(e.g., \code{"ENTREZID"}). Default is \code{"ENTREZID"}.}

\item{readable}{Logical. Whether to convert the enrichment result IDs back to a readable format (e.g., SYMBOL).
Only applicable for GO and KEGG analysis. Default is \code{TRUE}.}

\item{organism}{Character. The KEGG organism code (e.g., \code{"hsa"} for human, \code{"mmu"} for mouse). Required when
performing KEGG enrichment. Default is \code{"hsa"}.}

\item{pvalueCutoff}{Numeric. The p-value cutoff for enriched terms to be included in the results. Default is \code{0.05}.}

\item{topn}{Integer or vector. The number of top enrichment results to extract. If a single value, it is applied
to all clusters. Otherwise, it should match the number of clusters. Default is \code{5}.}

\item{seed}{Numeric. Seed for random operations to ensure reproducibility. Default is \code{5201314}.}

\item{add.gene}{Logical. Whether to include the list of genes associated with each enriched term in the results.
Default is \code{FALSE}.}

\item{use_internal_data}{Logical, use KEGG.db or latest online KEGG data for enrichKEGG function.
Default is \code{FALSE}.}

\item{heatmap.type}{Character. The type of heatmap visualization to use when input data is a \code{CellDataSet} object.
Options include:
\itemize{
\item \code{"plot_pseudotime_heatmap2"}
\item \code{"plot_genes_branched_heatmap2"}
\item \code{"plot_multiple_branches_heatmap2"}
}}

\item{...}{Additional arguments passed to plot_pseudotime_heatmap2/plot_genes_branched_heatmap2/plot_multiple_branches_heatmap2 functions.}
}
\value{
a data.frame.
}
\description{
Perform GO/KEGG Enrichment Analysis for Multiple Clusters
}
\author{
JunZhang

This function performs Gene Ontology (GO) or KEGG enrichment analysis, or custom gene set enrichment,
on clustered genes. It supports multiple clusters, incorporating cluster-specific results into its analysis.
}