Package index • NMFscape

Main Functions

Core NMF and consensus NMF functions

runNMFscape(): Run NMFscape Non-negative Matrix Factorization on SingleCellExperiment objects

runConsensusNMF(): Run Consensus Non-negative Matrix Factorization on SingleCellExperiment objects

Standard NMF Accessors

Access standard NMF results

getBasis(): Extract NMF basis matrix from SingleCellExperiment object

getCoefficients(): Extract NMF coefficient matrix from SingleCellExperiment object

getTopFeatures(): Calculate feature loadings (which genes contribute most to each factor)

reconstructNMF(): Reconstruct original matrix from NMF factors

Consensus NMF Accessors

Access consensus NMF results

getConsensusGEPs(): Extract consensus gene expression programs (GEPs) from cNMF results

getGEPUsage(): Extract GEP usage matrix from cNMF results

getStabilityMetrics(): Get stability metrics from cNMF results

getOptimalK(): Get optimal k value from cNMF results

getTopGEPFeatures(): Get top features for each consensus gene expression program

getConsensusNMFInfo(): Get consensus NMF information and parameters

getAvailableK(): Get available k values from cNMF results

Visualization

Plotting functions for diagnostics and results

vizUMAP(): Visualize NMF programs on UMAP coordinates

vizDimRed(): Visualize NMF programs on dimension reduction plots

plotStability(): Plot stability metrics from consensus NMF

plotStabilityComparison(): Plot comparison of stability metrics across different k values

plotGEPs(): Plot gene expression programs (GEPs) heatmap

plotGEPUsage(): Plot GEP usage in reduced dimension space

GO Enrichment Analysis

Gene Ontology enrichment and visualization functions

FindAllDEPs(): Find All Differentially Expressed Programs (1-vs-all analysis)

runProgramGOEnrichment(): Run Gene Ontology enrichment on NMF program gene sets

prepareProgramGeneSets(): Prepare gene sets for enrichment analysis from NMF programs

plotGOBarChart(): Plot GO Enrichment Bar Chart

plotGODotPlot(): Plot GO Enrichment Dot Plot

plotGONetwork(): Plot GO Network

plotDEPsDots(): Visualize Differentially Expressed Programs with dot plot

plotDEPsVolcano(): Visualize Differentially Expressed Programs with volcano plots

plotProgramGenes(): Visualize top genes per NMF program with heatmap

plotMultipleProgramsGO(): Plot Multiple Programs GO Comparison

saveGOPlotsToPDF(): Save GO Plots to PDF