--- a
+++ b/man/extract_ntop_pathways.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/EnrichmentSpiralize.R
+\name{extract_ntop_pathways}
+\alias{extract_ntop_pathways}
+\title{Extract and Store Top Pathways for Each Sample}
+\usage{
+extract_ntop_pathways(ssgsea_kegg, nTop = 5)
+}
+\arguments{
+\item{ssgsea_kegg}{Dataframe containing SSGSEA KEGG results with samples as columns and pathways as rows.}
+
+\item{nTop}{Integer, number of top pathways to select for each sample.}
+}
+\value{
+A dataframe with columns 'Pathway', 'Sample', and 'Value' representing the top pathways for each sample.
+}
+\description{
+This function processes a dataframe containing SSGSEA KEGG results. It allows specifying the number
+of top pathways to extract for each sample based on their scores, and stores these in a new dataframe
+with sample names and pathway scores.
+}
+\examples{
+# Example: Generating input data for the extract_ntop_pathways function
+
+# Define example pathways
+pathways <- c("Pathway_A", "Pathway_B", "Pathway_C", "Pathway_D", "Pathway_E",
+              "Pathway_F", "Pathway_G", "Pathway_H", "Pathway_I", "Pathway_J")
+
+# Define example samples
+samples <- c("Sample_1", "Sample_2", "Sample_3")
+
+# Generate random SSGSEA KEGG scores between 0 and 1
+set.seed(123)  # For reproducibility
+ssgsea_scores <- matrix(runif(length(pathways) * length(samples), min = 0, max = 1),
+                        nrow = length(pathways), ncol = length(samples),
+                        dimnames = list(pathways, samples))
+
+# Convert to a data frame
+ssgsea_kegg <- as.data.frame(ssgsea_scores)
+
+# Extract the top 3 pathways for each sample
+top_pathways <- extract_ntop_pathways(ssgsea_kegg, nTop = 3)
+
+}