NMFprofileR

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Overview

NMFprofileR is an R package for comprehensive multi-rank Non-negative Matrix Factorization (NMF) analysis of transcriptomic data. It provides automated rank estimation, factor-specific gene assignment, gene set enrichment analysis, and publication-quality plots for consolidated summary and consensus maps.

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Features

• Multi-rank NMF with reproducible results (brunet, lee, and others).
• Per-factor basis gene extraction using all genes assigned to each factor.
• Automated generation of:
  • Rank survey plots
  • Consensus maps
  • Factor correspondence heatmaps
  • Consolidated summary metrics
• Supports user-defined gene backgrounds for enrichment analysis.
• Clean output directories for reproducible workflows.

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Installation

Install directly from GitHub using devtools:

# install.packages("devtools")
devtools::install_github("MilesGithub/NMFprofileR")

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Usage

library(NMFprofileR)

# Load example expression data (genes x samples)
data("example_expression_data")

# Run the NMFprofileR pipeline
results <- NMFprofileR(
  expression_data          = example_expression_data,
  nmf_rank                 = 2:5,
  output_prefix            = "results/NMF",
  gene_list_filter_file    = NULL,
  nmf_method               = "brunet",
  nmf_nrun                 = 20,
  gprofiler_organism       = "hsapiens",
  gprofiler_sources        = c("GO:BP","GO:MF","GO:CC","REAC","TF"),
  gprofiler_cutoff         = 0.05
)

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Output

The pipeline generates:

• results/NMF/nmf_core/ — NMF R objects per rank.
• results/NMF/basis_genes/ — Per-factor gene assignments (all genes).
• results/NMF/enrichment/ — Factor-specific and combined enrichment results.
• results/NMF/plots/ — Publication-quality heatmaps and consensus plots.
• results/NMF/summaries/ — Consolidated summary of all ranks and factors.

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Example Plots

• Rank Survey Plot – metrics across tested ranks.
• Consensus Map – reproducibility of factorization.
• Factor Correspondence Heatmap – identifies similar factors across ranks.
• Consolidated Summary Heatmap – combined factor-level metrics for all ranks.

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Citation

Miles Mee, 2025. NMFprofileR: Comprehensive multi-rank NMF analysis and enrichment in R. GitHub repository: https://github.com/MilesGithub/NMFprofileR

Also cite underlying methods:

• Gaujoux, R., & Seoighe, C. (2010). A flexible R package for nonnegative matrix factorization. BMC Bioinformatics, 11, 367.
• Raudvere, U., Kolberg, L., Kuzmin, I., Arak, T., Adler, P., Peterson, H., & Vilo, J. (2019). g:Profiler: a web server for functional enrichment analysis and conversions of gene lists. Nucleic Acids Research, 47(W1), W191–W198.

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License

MIT License — see LICENSE.

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Contact

Open an issue on GitHub or contact Miles Mee at miles.william.mee@gmail.com.