Creates a heatmap showing expression of top unique genes per NMF program across different cell types. Helps interpret the biological meaning of programs.
Usage
plotProgramGenes(
x,
cell_type_col,
nmf_name = "NMF",
n_genes = 5,
max_genes = 50,
assay_name = "logcounts",
scale_rows = TRUE,
show_programs = TRUE
)Arguments
- x
A SingleCellExperiment object with NMF results
- cell_type_col
Character, column name in colData containing cell type labels
- nmf_name
Character, name of NMF result to use (default "NMF")
- n_genes
Integer, number of top genes per program to include (default 5)
- max_genes
Integer, maximum total genes to show (default 50)
- assay_name
Character, which assay to use for expression values (default "logcounts")
- scale_rows
Logical, whether to scale rows (genes) for visualization (default TRUE)
- show_programs
Logical, whether to show program annotations on heatmap (default TRUE)
Examples
sce <- runNMFscape(sce, k = 8)
#> Error: object 'sce' not found
plotProgramGenes(sce, "cell_type", n_genes = 8, max_genes = 40)
#> Error: object 'sce' not found