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Visualize NMF programs on UMAP coordinates

Source: R/vizUMAP.R
vizUMAP.Rd

Convenience function to plot NMF program usage on UMAP coordinates. This is a wrapper around vizDimRed() specifically for UMAP plotting.

Usage

vizUMAP(
  x,
  nmf_name = "NMF",
  program = 1,
  point_size = 0.8,
  alpha = 1,
  color_scale = "viridis",
  title = NULL
)

Arguments

x

A SingleCellExperiment object with NMF results and UMAP coordinates

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" (default "viridis")

title

Character, plot title (if NULL, auto-generates from program name)

Value

A ggplot object

Examples

# Basic usage
library(scuttle)
sce <- mockSCE()
sce <- logNormCounts(sce)
sce <- runNMFscape(sce, k = 5)
#> Running NMF with k=5 factors...
#> 
#> iter |      tol 
#> ---------------
#>    1 | 8.25e-01
#>    2 | 4.25e-02
#>    3 | 2.05e-02
#>    4 | 1.09e-02
#>    5 | 6.73e-03
#>    6 | 4.52e-03
#>    7 | 3.20e-03
#>    8 | 2.34e-03
#>    9 | 1.76e-03
#>   10 | 1.34e-03
#>   11 | 1.03e-03
#>   12 | 7.86e-04
#>   13 | 5.99e-04
#>   14 | 4.52e-04
#>   15 | 3.41e-04
#>   16 | 2.59e-04
#>   17 | 2.00e-04
#>   18 | 1.57e-04
#>   19 | 1.25e-04
#>   20 | 1.01e-04
#>   21 | 8.34e-05
#>   22 | 6.86e-05
#>   23 | 5.74e-05
#>   24 | 4.79e-05
#>   25 | 4.01e-05
#>   26 | 3.40e-05
#>   27 | 2.90e-05
#>   28 | 2.48e-05
#>   29 | 2.10e-05
#>   30 | 1.79e-05
#>   31 | 1.50e-05
#>   32 | 1.27e-05
#>   33 | 1.10e-05
#>   34 | 9.67e-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
vizUMAP(sce, program = 1)
#> Error in vizDimRed(x = x, dimred = "UMAP", nmf_name = nmf_name, program = program,     point_size = point_size, alpha = alpha, color_scale = color_scale,     title = title, dims = c(1, 2)): Dimension reduction 'UMAP' not found in reducedDims(x). Available: NMF

# Plot specific program by name with custom styling
vizUMAP(sce, program = "NMF_4", color_scale = "plasma", point_size = 1.2)
#> Error in vizDimRed(x = x, dimred = "UMAP", nmf_name = nmf_name, program = program,     point_size = point_size, alpha = alpha, color_scale = color_scale,     title = title, dims = c(1, 2)): Dimension reduction 'UMAP' not found in reducedDims(x). Available: NMF