% 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)

}