--- a
+++ b/man/extract_positive_pathways.Rd
@@ -0,0 +1,43 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/EnrichmentSpiralize.R
+\name{extract_positive_pathways}
+\alias{extract_positive_pathways}
+\title{Extract Positive Pathways from SSGSEA Results and Select Random Samples}
+\usage{
+extract_positive_pathways(ssgsea_kegg, max_paths_per_sample = 5)
+}
+\arguments{
+\item{ssgsea_kegg}{A matrix or data frame with pathways as rows and samples as columns.}
+
+\item{max_paths_per_sample}{Integer, maximum number of pathways to select per sample.}
+}
+\value{
+A data frame with selected pathways, samples, and their corresponding values.
+}
+\description{
+This function processes the results of SSGSEA, specifically focusing on KEGG pathways.
+It extracts pathways with positive values from each sample and randomly selects a subset of them.
+}
+\examples{
+# Example: Generating input data for the extract_positive_pathways function
+
+# Define example pathways
+pathways <- c("Pathway_1", "Pathway_2", "Pathway_3", "Pathway_4", "Pathway_5",
+              "Pathway_6", "Pathway_7", "Pathway_8", "Pathway_9", "Pathway_10")
+
+# Define example samples
+samples <- c("Sample_A", "Sample_B", "Sample_C")
+
+# Generate random SSGSEA KEGG scores including both positive and negative values
+set.seed(456)  # For reproducibility
+ssgsea_scores <- matrix(rnorm(length(pathways) * length(samples), mean = 0, sd = 1),
+                        nrow = length(pathways), ncol = length(samples),
+                        dimnames = list(pathways, samples))
+
+# Convert to a data frame
+ssgsea_kegg <- as.data.frame(ssgsea_scores)
+
+# Use the extract_positive_pathways function to extract up to 3 positive pathways per sample
+selected_positive_pathways <- extract_positive_pathways(ssgsea_kegg, max_paths_per_sample = 3)
+
+}