Plot NMF program usage on dimension reduction coordinates (UMAP, PCA, etc.) with flexible color mapping and customization options.
Usage
vizDimRed(
x,
dimred = "UMAP",
nmf_name = "NMF",
program = 1,
point_size = 0.8,
alpha = 1,
color_scale = "viridis",
title = NULL,
dims = c(1, 2)
)Arguments
- x
A SingleCellExperiment object with NMF results and dimension reduction
- dimred
Character, name of dimension reduction to use (default "UMAP")
- nmf_name
Character, name of NMF result to use (default "NMF")
- program
Character or integer, which NMF program to plot (e.g., "NMF_1", "NMF_4", or 4)
- point_size
Numeric, size of points (default 0.8)
- alpha
Numeric, transparency of points (default 1.0)
- color_scale
Character, color scale to use: "viridis", "plasma", "inferno", "magma", or custom (default "viridis")
- title
Character, plot title (if NULL, auto-generates from program name)
- dims
Integer vector of length 2, which dimensions to plot (default c(1,2))
Examples
# Basic usage
library(scuttle)
sce <- mockSCE()
sce <- logNormCounts(sce)
sce <- runNMFscape(sce, k = 5)
#> Running NMF with k=5 factors...
#>
#> iter | tol
#> ---------------
#> 1 | 8.10e-01
#> 2 | 4.09e-02
#> 3 | 1.84e-02
#> 4 | 9.90e-03
#> 5 | 6.27e-03
#> 6 | 4.41e-03
#> 7 | 3.29e-03
#> 8 | 2.52e-03
#> 9 | 1.92e-03
#> 10 | 1.47e-03
#> 11 | 1.13e-03
#> 12 | 8.68e-04
#> 13 | 6.67e-04
#> 14 | 5.15e-04
#> 15 | 4.01e-04
#> 16 | 3.06e-04
#> 17 | 2.38e-04
#> 18 | 1.85e-04
#> 19 | 1.46e-04
#> 20 | 1.18e-04
#> 21 | 9.48e-05
#> 22 | 7.74e-05
#> 23 | 6.41e-05
#> 24 | 5.35e-05
#> 25 | 4.53e-05
#> 26 | 3.83e-05
#> 27 | 3.29e-05
#> 28 | 2.82e-05
#> 29 | 2.43e-05
#> 30 | 2.11e-05
#> 31 | 1.86e-05
#> 32 | 1.64e-05
#> 33 | 1.45e-05
#> 34 | 1.30e-05
#> 35 | 1.17e-05
#> 36 | 1.05e-05
#> 37 | 9.55e-06
#> NMF completed. Results stored in reducedDim(x, 'NMF')
#> Basis matrix stored in metadata(x)$NMF_basis
sce <- runUMAP(sce)
#> Error in runUMAP(sce): could not find function "runUMAP"
# Plot NMF program 1 on UMAP
vizDimRed(sce, program = 1)
#> Error in vizDimRed(sce, program = 1): Dimension reduction 'UMAP' not found in reducedDims(x). Available: NMF
# Plot specific program by name
vizDimRed(sce, program = "NMF_4")
#> Error in vizDimRed(sce, program = "NMF_4"): Dimension reduction 'UMAP' not found in reducedDims(x). Available: NMF
# Use PCA instead of UMAP
sce <- runPCA(sce)
#> Error in runPCA(sce): could not find function "runPCA"
vizDimRed(sce, dimred = "PCA", program = 2)
#> Error in vizDimRed(sce, dimred = "PCA", program = 2): Dimension reduction 'PCA' not found in reducedDims(x). Available: NMF